Just a quick tip: Repairing the permissions on an OS X disk can be done from the command-line as well. The only caveat, you have to know the device of the volume. Getting the right device is easy:
diskutil list
The device-node in question is in the column titled IDENTIFIER. The device-path to use is the one with the name of the volume, e.g. if the column reads disk0s2, then the command would be:
diskutil repairPermissions /dev/disk0s2
You should see some kind of progress-bar in ASCII.
One thing to note though: Using the command does not prevent the “meditation” of the program after 20%. I’d be interested what the system is doing while it seems to mull over something when it is supposed to repair the permissions. 