Q: Repair Permission

You are basically wasting your time. Whatever you read that said to repair permissions is a good thing isn't very knowledgeable.

Don't worry about this, there are many in Mavericks and Mountain Lion  that hopefully will be sorted with future updates.

This is one of the permissions you can ignore  http://support.apple.com/kb/TS1448

About repair pernissions: http://support.apple.com/kb/HT1452

Take a good read of the link leroydouglas posted. It covers all the aspect of repair permissions.

OS X does get fragmented but not in the same way as Windows does (to long to go into). But OS X doesn't need defragging like windows does. The basic reason is even though OS X will place files All Over the drive none of them are really Fragmented. They are Whole Files not parts of file like in Windows.