AFter update to 10.6.5 - REPAIR PERMISSION prob

I ran the repair permissions after upgrade (SU)- it says repaired, so tho't I'd rerun it to see if any changes. It seems NOTHING was repaired as the same thing it said it repaired on first run it said needed repairing on second-here's two runs-I glanced over and they sure look the same to me:
Repairing permissions for “Macintosh HD”
User differs on "private/var/at", should be 0, user is 1.
Repaired "private/var/at".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r".
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib", should be 0, user is 95.
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib".
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries", should be 0, user is 95.
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries".
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar".
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 .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries".
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 .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar".
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 .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib".
ACL found but not expected on "private/etc/apache2/users".
Repaired "private/etc/apache2/users".
ACL found but not expected on "Library/Preferences/Audio".
Repaired "Library/Preferences/Audio".
ACL found but not expected on "System/Library/Keychains/X509Anchors".
Repaired "System/Library/Keychains/X509Anchors".
Warning: SUID file "System/Library/Printers/IOMs/LPRIOM.plugin/Contents/MacOS/LPRIOMHelper" has been modified and will not be repaired.
ACL missing on "Users".
Repaired "Users".
ACL found but not expected on "private/etc/hostconfig".
Repaired "private/etc/hostconfig".
ACL found but not expected on "private/etc/master.passwd".
Repaired "private/etc/master.passwd".
ACL found but not expected on "private/etc/passwd".
Repaired "private/etc/passwd".
ACL found but not expected on "private/var/db/launchd.db/com.apple.launchd".
Repaired "private/var/db/launchd.db/com.apple.launchd".
ACL found but not expected on "private/var/yp/binding".
Repaired "private/var/yp/binding".
Warning: SUID file "usr/sbin/scselect" has been modified and will not be repaired.
Permissions repair complete
Repairing permissions for “Macintosh HD”
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r".
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib", should be 0, user is 95.
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib".
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries", should be 0, user is 95.
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries".
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar".
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 .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries".
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 .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar".
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 .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib".
ACL found but not expected on "private/etc/apache2/users".
Repaired "private/etc/apache2/users".
ACL found but not expected on "Library/Preferences/Audio".
Repaired "Library/Preferences/Audio".
ACL found but not expected on "System/Library/Keychains/X509Anchors".
Repaired "System/Library/Keychains/X509Anchors".
Warning: SUID file "System/Library/Printers/IOMs/LPRIOM.plugin/Contents/MacOS/LPRIOMHelper" has been modified and will not be repaired.
ACL missing on "Users".
Repaired "Users".
ACL found but not expected on "private/etc/hostconfig".
Repaired "private/etc/hostconfig".
ACL found but not expected on "private/etc/master.passwd".
Repaired "private/etc/master.passwd".
ACL found but not expected on "private/etc/passwd".
Repaired "private/etc/passwd".
ACL found but not expected on "private/var/db/launchd.db/com.apple.launchd".
Repaired "private/var/db/launchd.db/com.apple.launchd".
ACL found but not expected on "private/var/yp/binding".
Repaired "private/var/yp/binding".
Warning: SUID file "usr/sbin/scselect" has been modified and will not be repaired.
Permissions repair complete

But it is COMPLETE. You asked it to start and it started, it processed the current security rules according to the BOM file for your level of OS (Such as 'Mac OS X Server 10.6.5 (10H574)' ) and made it to the end.
The previous poster was technically correct even if not terribly helpful in that the messages are telling you that DiskUtil found an difference between the BOM list and your SYSTEM files and either fixed it by making a change or it was a skippable change and so everything passed (did not make an error condition) and so it is now COMPLETE.
Our favorite OS is VERY complex, with a mish-mash of rules that govern many things including its rights assignments and also by having a legacy of these rules that started WAAY back with 10.0 Beta back in March 2001 (and further back even to Server 1.0 but that was even less compatible with the line of 10.x , but i digress) so the bottom line statement is, it is done, it has fixed as much as it could fix, and it was successful in fixing what it could fix.
HTH,
Peter

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