DiskUtility won't repair, but ...

... my new MacBook Pro runs perfectly. I get a long list like this:
Repairing permissions for “Macintosh HD”
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/dt.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/dt.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar".
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".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/management- agent.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/management- agent.jar".
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".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jce.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jce.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/management -agent.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/management -agent.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/b lacklist", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/b lacklist".
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/Home/lib/security/cacerts", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/Support/Deploy.bundle/Contents/Home/lib/security/cacerts".
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/Support/Deploy.bundle/Contents/Resources/Java/deploy.jar".
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/dt.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/dt.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.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 ".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/management-a gent.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/management-a gent.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".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/dt.jar", should be lrwxr-xr-x , they are -rw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/dt.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/jce.jar", should be lrwxr-xr-x , they are -rw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/jce.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/management- agent.jar", should be lrwxr-xr-x , they are -rw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/management- agent.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/security/bl acklist", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/security/bl acklist".
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", should be drwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle".
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".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Home/lib/security/cacerts", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Home/lib/security/cacerts".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/libdeploy.jnilib".
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Permissions repair complete
And if I run Repair again, I get the same info, which is very different from my old PowerBook where the permissions were always clean. I get the same results when I run DU from the install DVD. Reason to try and fix?, worry?

peejay33 wrote:
... my new MacBook Pro runs perfectly.
Then why would you thingk the rest matters?
Repairing permissions is just a troubleshooting technique if you are experiencing file access problems. Also, it only affects specific locations in the System and does not affect your user folder at all.
The reason for the output is that the recent updates to Snow Leopard changed things that Repair Permissions doesn't know about, so it flags them as things that "differ." Here is the list of Items you can safely ignore. Also, see here: http://support.apple.com/kb/ht1452

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