Disk Utility can't fix the following...

I've had a crash problem with InDesign (on one document in particular), and repeatedly running Disk Utility results in:

Verify permissions for “Macintosh HD”
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .

Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrw-r--r-- .

Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.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/ARDAgent" has been modified and will not be repaired.

Permissions verification complete

When I repair the permissions, all but the last one are fixed, but show up again when I verify. Is there something else I can do to fix these files?

Thanks,
Bill

G'day and welcome to the forums.

They do not need fixing. Have a read of this:-

http://support.apple.com/kb/ts1448

If this still worries you download a utility called ACLr8 and run that.

http://osx.iusethis.com/app/aclr8