Disk Utility: Java VM Permission errors keep coming back

Question

Hello everyone,
I have a problem with my permissions. When I run Disk Utility I always get the same errors, I repair them and DU says they are repaired. Yet, if I run Disk Utility again (even right after a repair), there they are again.
It's a never-ending story: I repair them, DU says they are repaired, but they keep coming back at every scan (even when I run multiple scan/repair cycles in a row).
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ", should be -rw-r--r-- , they are lrwxr-xr-x .
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib", should be 95, user is 0.
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries", should be 95, user is 0.
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
I checked them against the safe-to-ignore list on http://support.apple.com/kb/TS1448 , but except for the last message (the SUID ARDAgent file) the other alerts regarding the JavaVM Framework seem not to be safe to ignore at all.
Does anybody know how to repair these permissions permanently (not just for three seconds)?
Thank you,
Daniele

Answer 1

Aha. Well, too much caution is better than none. I might suggest you skip the defragging unless you use very large files - 20 MBs and larger - with frequent changes. Unlike Windows OS X defrags files under 20 MBs on the fly to minimize fragmentation. Maintaining an adequate amount of free space on your hard drive will virtually eliminate fragmentation. We suggest 15 GBs or 10% of the hard drive's capacity, whichever is greater, should be maintained as free space. Fragmentation can become an issue as the amount of free space declines. The risks become greatest when free space drops to 5 GB or less.
We recommend repairing permissions and the hard drive prior to installing any new system updates. Repairing permissions after the installation is also a good idea since it's possible that fixes to Disk Utility may remove extraneous but innocuous "errors" being reported each time you repair permissions.
Some other occasional maintenance can't hurt. See the following:
Kappy's Personal Suggestions for OS X Maintenance
For disk repairs use Disk Utility. For situations DU cannot handle the best third-party utilities are: Disk Warrior; DW only fixes problems with the disk directory, but most disk problems are caused by directory corruption; Disk Warrior 4.x is now Intel Mac compatible. TechTool Pro provides additional repair options including file repair and recovery, system diagnostics, and disk defragmentation. TechTool Pro 4.5.1 or higher are Intel Mac compatible; Drive Genius is similar to TechTool Pro in terms of the various repair services provided. Versions 1.5.1 or later are Intel Mac compatible.
OS X performs certain maintenance functions that are scheduled to occur on a daily, weekly, or monthly period. The maintenance scripts run in the early AM only if the computer is turned on 24/7 (no sleep.) If this isn't the case, then an excellent solution is to download and install a shareware utility such as Macaroni, JAW PseudoAnacron, or Anacron that will automate the maintenance activity regardless of whether the computer is turned off or asleep. Dependence upon third-party utilities to run the periodic maintenance scripts had been significantly reduced in Tiger and Leopard. These utilities have limited or no functionality with Snow Leopard and should not be installed.
OS X automatically defrags files less than 20 MBs in size, so unless you have a disk full of very large files there's little need for defragmenting the hard drive. As for virus protection there are few if any such animals affecting OS X. You can protect the computer easily using the freeware Open Source virus protection software ClamXAV. Personally I would avoid most commercial anti-virus software because of their potential for causing problems.
I would also recommend downloading the shareware utility TinkerTool System that you can use for periodic maintenance such as removing old logfiles and archives, clearing caches, etc. Other utilities are also available such as Onyx, Leopard Cache Cleaner, CockTail, and Xupport, for example.
For emergency repairs install the freeware utility Applejack. If you cannot start up in OS X, you may be able to start in single-user mode from which you can run Applejack to do a whole set of repair and maintenance routines from the commandline. Note that AppleJack 1.5 is required for Leopard. AppleJack 1.6 is compatible with Snow Leopard.
When you install any new system software or updates be sure to repair the hard drive and permissions beforehand. I also recommend booting into safe mode before doing system software updates.
Get an external Firewire drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
Backuplist
Carbon Copy Cloner
Data Backup
Deja Vu
iBackup
JaBack
Silver Keeper
MimMac
Retrospect
Super Flexible File Synchronizer
ynchronizer
SuperDuper!
Synchronize Pro! X
SyncTwoFolders
Synk Pro
Synk Standard
Tri-Backup
Visit The XLab FAQs and read the FAQs on maintenance, optimization, virus protection, and backup and restore.
Additional suggestions will be found in Mac Maintenance Quick Assist.
Referenced software can be found at www.versiontracker.com and www.macupdate.com.
Continue enjoying your trouble free Mac. I've used them for over 20 years and love them. Currently have six of them all of which have never been a problem. Still have my 2006 MBP Core 2 Duo running good as new.