If any of the messages when you repaired permissions were similar to "We are using special permissions on (...)" then nothing was repaired at all (nor does anything need repairing). Those are simply informational messages that will appear every single time you repair permissions, and do not indicate that any permissions were incorrect or that any permissions were repaired. They simply inform you that Mac OS X is using some non-standard permissions for certain files and directories, and those messages can safely be ignored. The wording of the messages is pretty self-explanatory and explicit and tell you exactly what is going on.
If a permission was truly repaired, Disk Utility will explicitly say so; something to the tune of "Permissions differ on (...)" followed by "Permissions repaired on (...)". If it doesn't explicitly say that a permission was wrong or if it doesn't explicitly say that a permission was repaired, then nothing was wrong and nothing was repaired. Pay special attention to the messages that Disk Utility tells you to see if anything was truly repaired or not.