Permissions not repairing with Disk Utility

Question

I booted off my internal backup drive to run Disk Utilities on my main drive as I've been having some display problems and wanted to check for viruses and check the integrity of my drive. No viruses, disc verifies OK, but I had a lot of permissions needing repair, which I did.
I then cleared history and ran Verify Permissions again and even though the repair said all permissions were repaired except the last SUID file, these 7 came back. I ran repair again. Disk Utility said all except SUID were repaired like before. Ran verify again and they same 7 plus SUID showed up needing the same repairs Disk Utility said it fixed twice before.
Is this indicative of a serious problem? Any ideas how to fix them? Do I even need to?
Have MacPro1,1 - Running OSX 10.6.7, 8 GB RAM
Thanks,
Steven
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ", should be -rw-r--r-- , they are lrw-r--r-- .
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 lrw-r--r-- .
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 lrw-r--r-- .
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 .
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/JavaPlugin Cocoa.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/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.

Answer 1

Thanks re permissions. I was going to try DiskWarior, to see if it could repair them, but won't now.
For viruses I ran MacScan. Only found some tracking cookies and removed them.
(PS: with the new Discussions points, is it better to click Correct Answer or Helpful Answer? I wanted to click both, but after clicking Helpful, Correct disappeared. Guess I should have clicked Correct for you. I assume this is how we acrue points?)
Thx,
S