Just to clarify: no permissions are repaired unless explicitly stated... something to the tune of "Permissions differ on [blah blah]" and then "Permissions repaired on [blah blah]."
If you're seeing messages like "We are using special permissions for [blah blah]", then it's quite obvious that the permissions are not being repaired, as it is not explicitly stated. These are simply informational messages alerting you to the fact that Mac OS X is using some non-standard permissions for certain files and directories. Those messages will appear every single time you run a repair permissions, no matter how many times you run it.