"Repair Disk Permissions" keeps showing the same permission differences

After the recent software updates, I suddenly cannot use my eFax Messenger. This happened once before, but I was able to fix the problem by running "Repair Disk Permissions" in Disk Utility.
This time "Repair Disk Permissions" did not fix the problem. Not only that, I noticed the same permission differences showing up again and again when I repeated Repair Disk Permissions.
Is the permissions database no longer accurate? Does anyone have any suggestions on how to resolve the permission differences? I notice that others have reported similar issues on this forum, but no definite resolutions have been posted.
Thanks for any help you can give me.

..."As long as the repair ends up with the message 'repairs complete' or words to that effect, you are OK."...
I don't know who started with the "repairs complete means everything is fine" business, but they were wrong and it is repeated far too often by too many people on this site.
Considering all of the messages erroneously being dismissed as "informational", it is ironic that the one message that is actually just "informational" is the one being given special significance.
The "repairs complete" message only means that the process has stopped. Try starting to repair permissions, then immediately click the "Stop permissions repair" button. Try logging in to a non-admin account and start a run -- when a password is requested, cancel. Try repairing permissions when there are problems with the permissions database. You will see messages such as "Stopped by user", "insufficient privileges" or "underlying task reported failure on exit, but in every case, the report will end with the "Permissions repair complete" message.
With respect to the OP's question, the overall "repair permissions" system as it stands in 10.5 has the appearance of an unfinished product (it received major revisions in the transition from 10.4). Without specific details, all anyone can say is that the error messages are likely false positives - except for any true positives that might be present among them.

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I routinely verify my HD and repair disk permissions. The latter often indicates repairs are needed, especially after installation of new software or updates (I repair before and after). But once repaired, if I verify the permissions they come out ok -- i.e., no repairs are needed. Until just recently. I am now getting the following message after repairing permissions:
Verify permissions for “Macintosh HD”
Determining correct file permissions.
Permissions differ on ./private/var/log/secure.log, should be -rw------- , they are -rw-r-----
Permissions verification complete
The privileges have been verified or repaired on the selected volume
If I verify permissions after repairing this, I get the same message again. So the repair is not holding. I am running OS X 10.4.11 and I recall that on earlier OS's there were sometimes innocuous repairs that kept being required, but that were not really a problem. But under 10.4.11 a repair has usually been good, and clears the deck. Until now. Any ideas?
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TIA
Message was edited by: Drake Bradley

Not to worry about it, that secure.log is a common one for that.
Repair Permissions checks Library>Receipts to find out the proper Permissions, that file's Permissions may exist in more than one and/or some OS component doesn't know the new/latest permissions when using it.

When I repair disk permissions I get the following:Repairing permissions for "MacIntosh HD" Determining correct file permissions. Permissions differ on ./Library/Widgets, should be drwxr-xr-x , they are drwxrwxr-x Owner and group corrected on ./Library/W

Repairing permissions for “MacIntosh HD”
Determining correct file permissions.
Permissions differ on ./Library/Widgets, should be drwxr-xr-x , they are drwxrwxr-x
Owner and group corrected on ./Library/Widgets
Permissions corrected on ./Library/Widgets
Permissions differ on ./System/Library/User Template, should be drwx------ , they are drwxr-xr-x
Owner and group corrected on ./System/Library/User Template
Permissions corrected on ./System/Library/User Template
Group differs on ./usr/bin/fetchmail, should be 0, group is 6
Permissions differ on ./usr/bin/fetchmail, should be -rwxr-xr-x , they are -rwxr-sr-x
Owner and group corrected on ./usr/bin/fetchmail
Permissions corrected on ./usr/bin/fetchmail
Permissions differ on ./usr/lib/php/build/Makefile.global, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/Makefile.global
Permissions corrected on ./usr/lib/php/build/Makefile.global
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Owner and group corrected on ./usr/lib/php/build/acinclude.m4
Permissions corrected on ./usr/lib/php/build/acinclude.m4
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Owner and group corrected on ./usr/lib/php/build/mkdep.awk
Permissions corrected on ./usr/lib/php/build/mkdep.awk
Permissions differ on ./usr/lib/php/build/phpize.m4, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/phpize.m4
Permissions corrected on ./usr/lib/php/build/phpize.m4
Permissions differ on ./usr/lib/php/build/scan_makefile_in.awk, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/scan_makefile_in.awk
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Permissions corrected on ./usr/lib/system/libmathCommon.A.dylib
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Owner and group corrected on ./usr/libexec/dumpemacs
Permissions corrected on ./usr/libexec/dumpemacs
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Then I sometimes get the brown screen that states,You must re-start your computer.
I have already zeroed out the hard drive and re-installed Panther and the upgrade Tiger disc.
I repair permissions using the Tiger disc upgrade.
Can anyone help me with this??

> I repair permissions using the Tiger disc upgrade.
One thing to note... When running Repair Disk Permissions, it is best to run it while started up normally, from your normal startup disk, not from a Mac OS X installation disc. The only time you should run it while started up from an installation disc is if some problem is preventing you from starting up normally. OTOH, Repair Disk can only be used when starting up from a different disk (such as an installation disc).
So, I would start up normally, run Disk Utility, and use Repair Disk Permissions on your normal startup disk.
NOTE: Repair Disk Permissions often gives alerts messages that can be ignored. They are more "informational," not serious errors.
http://support.apple.com/kb/TS1448
You should still run it periodically. When you run it, what needs to be repaired has been repaired; consider the rest of it an FYI. I've never experience a problem, where a Repair Disk Permissions message actually caused a problem. But, if you ever get an error while running Repair Disk (or Verify Disk), that is usually a serious problem.

I ran a repair disk permissions and got the following:

I ran a repair disk permissions on my mack book and i got the following message: Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent” has been modified and will not be repaired. What are the implications?

These are innocuous messages, not errors. The will be recurring but are harmless and will not affect your computer. They can be ignored.

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Thanks for your advice, I still have an issue:
-after the first repair disk permission "stalled" process, I exited Disk Utility and cold booted the machine after I had disconnected all external devices other than the original iMac keyboard
-obtained the combo patch for 10.4.7 from the Apple download site (it had already been installed but I reinstalled per your advice)
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- I pushed the "stop disk permission repair" button, then quit disk utility, then cold booted the machine again.
-re-applied combo patch as above, then cold booted the machine
-ran disk utility from the original iMac install #1 disk, ran "repair disk permissions", and then received the same error message as above.
- I then just quit Disk Utility and cold booted the machine again and went about my business. There does not seem to be any problem with the machine (was not before, but I ran repair permissions thinkging this was a routine maintenance taks that should be run)
- in my prior search of the knowledge base, I found the following information about repair disk permissions:
Location: http://discussions.apple.com/thread.jspa?messageID=607495&#607495
How often should I Repair Permissions?
You do not need to Repair Permissions on a regular basis.
There are only three occasions you need to do this:
1. When you have just installed something that required you to run an Installer, rather than just copying some software to a folder. This should be done for both Apple and non-Apple software.
2. When you have been working on your OS X files or folders while booted from OS 9, or remotely connected via a non-OS X machine, since OS 9 and other systems do not handle OS X's permissions correctly.
3. The other case is if your system is behaving strangely, when you should run Disk Repair from your CD followed by Repair Permissions. This is just to eliminate these things before going on to further trouble-shooting.
Otherwise you can happily forget about Permissions!"
So, it would appear I do not need to do anything else; the machine seems to be working properly. Is there anything else I need to do? thanks for the help! Bob

"Repair Disk Permissions" keeps showing the same permission differences

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