Results from permissions repair: Warning...

Warning: SUID file "System/Library/CoreServices/Expansion Slot Utility.app/Contents/Resources/PCIELaneConfigTool" has been modified and will not be repaired.
What is the problem with this result if any?

You always will get a bunch of warnings from repair permissions.
For example,
Disk Utility's Repair Disk Permissions messages that you can safely ignore

Similar Messages

Strange output from permissions repair

This not so much a problem but a question. When I did a routine permissions repair, I got the following message:
Repairing permissions for “Startup HD”
Warning: SUID file "usr/libexec/load_hdi" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/Resources /DiskManagementTool" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/Reso urces/Locum" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/readconf ig" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/writecon fig" has been modified and will not be repaired.
Warning: SUID file "usr/libexec/authopen" has been modified and will not be repaired.
Warning: SUID file "System/Library/CoreServices/Finder.app/Contents/Resources/OwnerGroupTool" has been modified and will not be repaired.
I have never seen a message that is headed, "Warning," and I don't know what it all means nor what to do about it if action is required.
Anyone know what this all means?
Thanks!

Well, you are right. Using the link you provided, the warning lines went away. I wonder how you knew to use that update other than the other? It took just short of 10 hours to do that download - more actually, but I didn't count the number of times I had to restart the download due to losing carrier during the download.
Apple is killing me with these enormous downloads. I live in a rural area, too far away from the road to use cable, so no broadband. The population density isn't there for Verizon or other carriers to make DSL available. I could use a satellite service but it is just way too expensive both with the monthly subscription price and with the investment in hardware needed. 109 megs to make this problem go away. Just not right. I think Apple forgets that many people do not have a high speed connections.
Anyway, thanks again.

Strange return from permissions repair

After having a problem with Software Update acting very strange, (it would seem like it was frozen, but actually was just extremely slow and unresponsive until it did whatever I had just clicked on) I did a permissions repair. I then downloaded the update and did the repair one more time. Both times I got an extrememly long list of changes and both times it included this:
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
The Remote Management part bothers me as I don't have anything set up for managing my computer other than from the keyboard. Can someone tell me what this is?
Thanks,
Rich

You can ignore SUID messages.
Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore

Same results for 'Permissions repair complete'

Very strange. I went to "First Aid' and clicked on "Repair Disc Permissions."
After a half hour or so, the report showed stuff like "Repaired "System/Library/Core Services/ . . . and ended with "Permissions repair complete."
I repeated the process and got the same results. In other words, the repair was not complete.

Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore
There is never a reason to repair permissions, except in the very rare case of a permission error, which you'll probably never see, or a boot failure. The built-in help for Disk Utility says:
Repairing disk permissions
If you see an alert or a message that says your permissions are set incorrectly, you can correct the disk’s permissions by clicking Repair Disk Permissions.
It’s not completely irrational to repair permissions after running a third-party installer, since such installers have been known to set incorrect permissions. Otherwise, repairing permissions is a complete waste of time.

Permissions Repair Warning Explanation Please

Hello Everyone,
It's been a while since I last posted on the Apple forums.
I just installed the Mac OSX 10.6.3 v1.1 Combo Update.
After doing so, I launched Disk Utility and ran "Repair Permissions".
At the very end of the permissions repair log, I found the following warning:
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Does anyone know what this means, or why it cannot be repaired?
If ARDAgent means Apple Remote Desktop Agent, as I suspect, then I am mystified, because, to my knowledge, I never use Apple Remote Desktop for anything, unless it is possibly used during the Software Update process without my knowledge.
I just want to know who has modified it, and why its permissions can't be repaired.
My computer specs are in my sig below.
Thanks!

Hello Niel. Thanks for your response. I just did some checking, and it appears that Mac users have been reporting this -- and similar messages by Disk Utility -- since at least three years ago when Leopard was first introduced.
In fact, I found a page here on the Apple site called "Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore".
It can be accessed at the following URL:
http://support.apple.com/kb/TS1448?viewlocale=en_US
So I suppose that, as you have stated, the message can be ignored.

Permissions Repair: Warning SUID file issue?

Greetings,
I have been having a sleep issue and an occasional error message that said the Time Machine backup could not be completed so I ran disk utility to repair permissions and this is what it said;
+Verify permissions for “Macintosh HD”+
+Permissions differ on "sbin/restore", should be -r-xr-xr-x , they are -r-sr-sr-x .+
+Warning: SUID file "sbin/restore" has been modified and will not be repaired.+
+Permissions differ on "sbin/rrestore", should be -r-xr-xr-x , they are -r-sr-sr-x .+
+Warning: SUID file "sbin/rrestore" has been modified and will not be repaired.+
+Permissions differ on "sbin/mount_smbfs", should be -r-xr-xr-x , they are -r-sr-xr-x .+
+Warning: SUID file "sbin/mount_smbfs" has been modified and will not be repaired.+
+Permissions differ on "usr/bin/smbutil", should be -r-xr-xr-x , they are -r-sr-xr-x .+
+Warning: SUID file "usr/bin/smbutil" has been modified and will not be repaired.+
+Group differs on "private/etc/cups", should be 0, group is 26.+
+Permissions verification complete+
Any ideas?
Thanks in advance - Scrags

it means that those files have set user id bits which shouldn't be there according to the permissions database. an s-bit makes a command run with the user id of the file for that command rather than the user invoking the command. for example, if you invoke unix restore command from terminal it ought to run as you. however, on your system it would run as root because the file /sbin/restore used to call this command is owned by root and has a user s-bit on it.
as i said this has nothing to do with your sleep issues but you might as well fix it.

Freeze then Permissions Repair "Warning'

I just had my 4 month old iMac completely freeze up after a Software Update. After I restarted I ran Repair permissions and (along with a bunch of other stuff) found the following message:
+Warning: SUID file "System/Library/CoreServices/Finder.app/Contents/Resources/OwnerGroupTool" has been modified and will not be repaired.+
+Group differs on "private/etc/cups", should be 0, group is 26.+
Is this anything I should be worried about?

No. See, Mac OS X 10.5- Disk Utility's Repair Disk Permissions reports issues with SUID files.

Permissions repair warning message

Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
...what does this mean and is it something I need to be concerned about?

You could try manually re-installing the Apple Remote Desktop 3.2.1 Client software. Then run the Disk Utility and repair permissions to see if the files were replaced with the correct permissions.
-Doug

After updating to Mavericks, get this during Permissions Repair: Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired"?

Repaired permissions once, got rid of the the previous iTunes errors. Cleared history and repaired again, still get:
Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent” has been modified and will not be repaired.
Any ideas?

I have just started seeing this message and, almost simultaneously, have started to have problems with various different apps crashing for no real reason. Just a coincidence?
For interest, SketchUp crashed with the message
"Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000f7f7fff9"
and QuarkXpress with the message
"Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000"
Am I just punching at shadows or could these be linked?
Hope someone can put my mind at rest.
Cheers....Scotty

Odd Result from Library Repair

Today, as I was requesting Aperture to export one photo to Facebook, I got the message that inconsistancies had been dedected. Although rare, this does happen from time to time, and Repair is always successful.
But this time, after the repair, I had a Recovered Project in the list of projects. It identified two files as problematic, and not displayable. Checking one of my clones of the Library, I found these to be two .mov files that in fact had not imported properly (but had on another Mac, into another library), and which were in the Trash in Aperture. Other photos were in the trash, yet only these two were plucked out for a Recovered Project. They remain in the Trash -- Curious!
Ernie

That is indeed curious. I'd expect in the "Recovered" project only originals, that are found as orphaned in the library, and have lost the connection to the versions, but not any corrupted files?

Disk Utility: Strange permissions repair results

Hi,
can anyone explain what these results mean? (D.U. cannot fix these errors.)
Thank you very much!
Peter
Repairing permissions for “iMac”
Warning: SUID file "usr/libexec/load_hdi" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/Resources /DiskManagementTool" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/Reso urces/Locum" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.
ACL found but not expected on "private/var/root/Library/Preferences".
ACL found but not expected on "private/var/root/Library".
ACL found but not expected on "private/var/root".
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/readconf ig" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/writecon fig" has been modified and will not be repaired.
Warning: SUID file "usr/libexec/authopen" has been modified and will not be repaired.
Warning: SUID file "System/Library/CoreServices/Finder.app/Contents/Resources/OwnerGroupTool" has been modified and will not be repaired.
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Permissions repair complete
Message was edited by: Peter R.
Forget it - one should always browse the posts before posting yourself. I found it. Sorry.

Please search the discussions before posting. This question has been asked and answerd dozens of times now.
You can safely ignore these messages, or you can download and manually install the 10.5.1 update to get rid of most of them.
http://www.apple.com/support/downloads/macosx1051update.html

Odd warning on permissions repair??

Hi -
Just installed SL and did the permissions repair... got a funny message on the imac (not MBP):
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Sounds like there is a vulnerability here... I don't have remote anything installed or activated (as least didn't intend to...even back to my mac)
should I worry about this? do anything?
thanks
tom

I see no such report on my system, so I'm guessing you may have done an upgrade from Leo, so this message could be caused by something residual from a Leo system. Such SUID messages are innocuous and can be ignored. Most likely it will recur each time you repair permissions.

Screen saver does not turn on. Have run the disc utility to repair disc permissions. Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.

screen saver does not turn on. Have run the disc utility to repair disc permissions. Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent” has been modified and will not be repaired.
I am running 10.9.1 software
Help Diggs1936

I would try reinstalling.
Reinstall Lion, Mountain Lion, or Mavericks without erasing drive
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
Repair
When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported then click on the Repair Permissions button. When the process is completed, then quit DU and return to the main menu. Select Restart from the Apple menu.
Reinstall Mountain Lion or Mavericks
OS X Mavericks- Reinstall OS X
OS X Mountain Lion- Reinstall OS X
OS X Lion- Reinstall Mac OS X
Note: You will need an active Internet connection. I suggest using Ethernet
if possible because it is three times faster than wireless.

Our MacbookPro began running very slow a few days ago. I ran disk repair, permissions repair, and restored the OS from the Apple server. Kernal_Task appears to be using excessive CPU.

EtreCheck version: 1.9.11 (43) - report generated June 15, 2014 at 7:45:12 AM CDT
Hardware Information:
          MacBook Pro - model: MacBookPro8,2
          1 2 GHz Intel Core i7 CPU: 4 cores
          4 GB RAM
Video Information:
          Intel HD Graphics 3000 - VRAM: 384 MB
          AMD Radeon HD 6490M - VRAM: 256 MB
System Software:
          OS X 10.9.3 (13D65) - Uptime: 0 days 6:20:35
Disk Information:
          TOSHIBA MK5065GSXF disk0 : (500.11 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) / [Startup]: 499.25 GB (294.57 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          MATSHITADVD-R   UJ-898
USB Information:
          Apple Inc. FaceTime HD Camera (Built-in)
          Apple Inc. BRCM2070 Hub
                    Apple Inc. Bluetooth USB Host Controller
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Computer, Inc. IR Receiver
Thunderbolt Information:
          Apple Inc. thunderbolt_bus
Gatekeeper:
          Mac App Store and identified developers
Kernel Extensions:
          [not loaded] com.intego.Family-Protector.safe-boot (10.7.5 - SDK 10.8) Support
Launch Daemons:
          [loaded] com.adobe.fpsaud.plist Support
          [running] com.intego.commonservices.daemon.integod.plist Support
          [running] com.intego.commonservices.daemon.taskmanager.plist Support
          [loaded] com.intego.commonservices.icalserver.plist Support
          [loaded] com.intego.commonservices.metrics.kschecker.plist Support
          [running] com.intego.Family-Protector.daemon.plist Support
          [running] com.intego.netbarrier.daemon.logger.plist Support
          [running] com.intego.netbarrier.daemon.monitor.plist Support
          [running] com.intego.netbarrier.daemon.plist Support
          [running] com.intego.netupdate.daemon.plist Support
          [running] com.intego.PersonalBackup.daemon.plist Support
          [loaded] com.intego.virusbarrier.daemon.emlparser.plist Support
          [running] com.intego.virusbarrier.daemon.logger.plist Support
          [running] com.intego.virusbarrier.daemon.plist Support
          [running] com.intego.virusbarrier.daemon.scanner.plist Support
          [running] com.intego.WashingMachine.service.plist Support
          [loaded] com.microsoft.office.licensing.helper.plist Support
Launch Agents:
          [running] com.intego.commonservices.integomenu.plist Support
          [loaded] com.intego.commonservices.taskmanager.plist Support
          [loaded] com.intego.commonservices.uninstaller.plist Support
          [running] com.intego.Family-Protector.agent.plist Support
          [loaded] com.intego.netbarrier.alert.plist Support
          [running] com.intego.netupdate.agent.plist Support
          [loaded] com.intego.personalbackup.agent.plist Support
          [loaded] com.intego.virusbarrier.alert.plist Support
User Launch Agents:
          [loaded] com.adobe.ARM.[...].plist Support
          [failed] com.apple.CSConfigDotMacCert-[...]@me.com-SharedServices.Agent.plist
User Login Items:
          VirusBarrier X6
          Antispam Engine
          iTunesHelper
          Activity Monitor
          Dropbox 1.40.07 PM
          AdobeResourceSynchronizer
Internet Plug-ins:
          JavaAppletPlugin: Version: Java 7 Update 51 Check version
          FlashPlayer-10.6: Version: 14.0.0.125 - SDK 10.6 Support
          Default Browser: Version: 537 - SDK 10.9
          AdobePDFViewerNPAPI: Version: 11.0.06 - SDK 10.6 Support
          AdobePDFViewer: Version: 11.0.06 - SDK 10.6 Support
          Flash Player: Version: 14.0.0.125 - SDK 10.6 Support
          QuickTime Plugin: Version: 7.7.3
          SharePointBrowserPlugin: Version: 14.3.9 - SDK 10.6 Support
          iPhotoPhotocast: Version: 7.0 - SDK 10.8
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
          AirPlay: Version: 2.0 - SDK 10.9
          AppleAVBAudio: Version: 203.2 - SDK 10.9
          iSightAudio: Version: 7.7.3 - SDK 10.9
iTunes Plug-ins:
          Quartz Composer Visualizer: Version: 1.4 - SDK 10.9
User Internet Plug-ins:
          WebEx64: Version: 1.0 - SDK 10.5 Support
3rd Party Preference Panes:
          Flash Player Support
Time Machine:
          Skip System Files: NO
          Mobile backups: OFF
          Auto backup: NO - Auto backup turned off
          Volumes being backed up:
                    Macintosh HD: Disk size: 464.96 GB Disk used: 190.62 GB
          Destinations:
                    My Passport [Local] (Last used)
                    Total size: 464.98 GB
                    Total number of backups: 19
                    Oldest backup: 2012-07-22 00:08:58 +0000
                    Last backup: 2014-06-14 17:10:32 +0000
                    Size of backup disk: Too small
                              Backup size 464.98 GB < (Disk used 190.62 GB X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
               3%          WindowServer
               1%          Activity Monitor
               1%          sysmond
               0%          ps
               0%          aosnotifyd
Top Processes by Memory:
          217 MB          mds_stores
          152 MB          com.apple.IconServicesAgent
          111 MB          Safari
          94 MB          softwareupdated
          49 MB          WindowServer
Virtual Memory Information:
          1018 MB          Free RAM
          1.41 GB          Active RAM
          604 MB          Inactive RAM
          1021 MB          Wired RAM
          1.65 GB          Page-ins
          0 B          Page-outs

I uninstalled all of the Intego products. I restarted the laptop, also ran disk repair and permissions repair again. Then allowed the machine to run with no apps active, just in case the OS was perfroming cleanup funtions. Results: No discernible improvement in performance. The kernal_task shows 500+% and the CPU graph shows 70%-80%.
There is one hardware issue: The magsafe battery port stopped charging the battery, so the laptop must be plugged in all the time.
Stan
EtreCheck version: 1.9.12 (48)
Report generated June 16, 2014 at 8:05:11 AM CDT
Hardware Information:
          MacBook Pro (15-inch, Early 2011) (Verified)
          MacBook Pro - model: MacBookPro8,2
          1 2 GHz Intel Core i7 CPU: 4 cores
          4 GB RAM
Video Information:
          Intel HD Graphics 3000 - VRAM: 384 MB
                    Color LCD 1440 x 900
          AMD Radeon HD 6490M - VRAM: 256 MB
System Software:
          OS X 10.9.3 (13D65) - Uptime: 0 days 21:8:4
Disk Information:
          TOSHIBA MK5065GSXF disk0 : (500.11 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) / [Startup]: 499.25 GB (293.77 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          MATSHITADVD-R   UJ-898
USB Information:
          Apple Inc. FaceTime HD Camera (Built-in)
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Inc. BRCM2070 Hub
                    Apple Inc. Bluetooth USB Host Controller
          Apple Computer, Inc. IR Receiver
Thunderbolt Information:
          Apple Inc. thunderbolt_bus
Gatekeeper:
          Mac App Store and identified developers
Launch Daemons:
          [loaded] com.adobe.fpsaud.plist Support
          [loaded] com.microsoft.office.licensing.helper.plist Support
User Launch Agents:
          [loaded] com.adobe.ARM.[...].plist Support
          [failed] com.apple.CSConfigDotMacCert-[...]@me.com-SharedServices.Agent.plist
User Login Items:
          VirusBarrier X6
          Antispam Engine
          iTunesHelper
          Activity Monitor
          Dropbox 1.40.07 PM
          AdobeResourceSynchronizer
Internet Plug-ins:
          JavaAppletPlugin: Version: Java 7 Update 51 Check version
          FlashPlayer-10.6: Version: 14.0.0.125 - SDK 10.6 Support
          Default Browser: Version: 537 - SDK 10.9
          AdobePDFViewerNPAPI: Version: 11.0.06 - SDK 10.6 Support
          AdobePDFViewer: Version: 11.0.06 - SDK 10.6 Support
          Flash Player: Version: 14.0.0.125 - SDK 10.6 Support
          QuickTime Plugin: Version: 7.7.3
          SharePointBrowserPlugin: Version: 14.3.9 - SDK 10.6 Support
          iPhotoPhotocast: Version: 7.0 - SDK 10.8
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
          AirPlay: Version: 2.0 - SDK 10.9
          AppleAVBAudio: Version: 203.2 - SDK 10.9
          iSightAudio: Version: 7.7.3 - SDK 10.9
iTunes Plug-ins:
          Quartz Composer Visualizer: Version: 1.4 - SDK 10.9
User Internet Plug-ins:
          WebEx64: Version: 1.0 - SDK 10.5 Support
3rd Party Preference Panes:
          Flash Player Support
Time Machine:
          Skip System Files: NO
          Mobile backups: OFF
          Auto backup: NO - Auto backup turned off
          Volumes being backed up:
                    Macintosh HD: Disk size: 464.96 GB Disk used: 191.37 GB
          Destinations:
                    My Passport [Local] (Last used)
                    Total size: 464.98 GB
                    Total number of backups: 19
                    Oldest backup: 2012-07-22 00:08:58 +0000
                    Last backup: 2014-06-14 17:10:32 +0000
                    Size of backup disk: Too small
                              Backup size 464.98 GB < (Disk used 191.37 GB X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
               5%          WindowServer
               3%          Activity Monitor
               3%          com.apple.WebKit.WebContent
               1%          hidd
               0%          sysmond
Top Processes by Memory:
          168 MB          softwareupdated
          139 MB          com.apple.IconServicesAgent
          123 MB          Safari
          119 MB          installd
          115 MB          mds_stores
Virtual Memory Information:
          498 MB          Free RAM
          1.62 GB          Active RAM
          927 MB          Inactive RAM
          998 MB          Wired RAM
          1.18 GB          Page-ins
          400 KB          Page-outs

Snow Leopard vs Long list of permissions repairs from 10.5.8 update

Hello Everyone,
My question is more of result of technical curiosity than anything else.
This is the first Mac that I have ever owned, therefore it must be said that I have never upgraded the Mac OS X operating system before.
It is well documented here in these forums that the latest update to Leopard (10.5.8) resulted in a rather long list of permissions repairs for many users, including myself. I have read through most of the posts regarding this issue and have even taken the advice which several of you have given to "reapply the combo update twice without doing a permissions repair"
Nevertheless, the list is still there, and according to most users, as well Apple, these can be ignored.
Having said that, I fully intend to upgrade to Snow Leopard when it is released on Friday...But, when I do, should I assume that since the upgrade essentially installs a new operating system, the permissions data base will show up without any permissions errors? Or is the only way to clear the permissions list, a "nuke and pave" (erase and install) which purportedly is not an option on the upgrade disc.
Most of you out there are smarter than I am and much more experienced with the process so any expert advice you may have would be appreciated.
Thanks in advance,
joe

In all the articles you've read through, it doesn't seem you quite understand the issue.
When they put out 10.5.8, Apple replaced a lot of files with links to the originals. The repair database doesn't know that they are supposed to be links. So, permission repair reports them as different than what it expects. There is nothing wrong. Stop repairing permissions for no reason and they won't bother you.
There is nothing you can do to cause them to go away. When Apple puts out another update, they will hopefully update the database so that it recognizes those links and doesn't report them. However, I expect at some time in the future, stuff will change and the permission database will not get updated, and you will see similar notifications.

Results from permissions repair: Warning...

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