That's the avg. quick and easy way to repair permissions. The problem with using that method is: As you repair permissions for your system, that same system is also running. So while you are running permission repairs, they still could be changing. That's why I only repair permissions from the OS X CD (or from one system to another), but not from system to self. To do it that way: Boot from the CD, go to Installer > Disk Utility, and continue using the quoted procedure.