if you cannot get Disk Utility to actually repair those permissions.

An Archive and Install "may" solve the problem but, it could be that more drastic measures will have to be taken.

Replacing the HD comes to mind, installing OS X from the OS X installation disks, and restoring from the Time Machine backup. (NOT the clone)
The clone contains the current errors while the TM backup does not contain any of the System, just the settings, applications and data.