"Repair Disk Permissions" doesn't seem to repair the permissions I tried repairing the permissions on the boot disk, resetting the Mac, and repairing the permissions on the boot disk. All times I repair the permissions, the list of the files that needs to be repaired is the same.

What does not allow to repair the permissions? What should I do to repair the permissions on the boot disk? Should I repair them from another Mac?
How do you know that your file's permissions are not OK?
What output does your repair permissions print? Any errors?

You could also try running the repair from the command-line if it would make any difference:
diskutil repairPermissions /Volumes/Macintosh\ HD/

Replace the volumes name.

You could also try running that with sudo or as root, to see if it changes anything.

Edit:
Actually, what you could be seeing is that some application is using the files that "need" to be repaired and thus Disk Utility can't repair them.
Try shutting all applications off and the running the repair