"Repair Disk Permissions" doesn't seem to repair the permissions
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