It repairs the UNIX-style permissions on your boot drive, if they somehow got changed. It's a good thing to do every month or so.
Open "Disk Utility" in the Utilities folder inside the Applications folder. Select your boot volume, then click "Repair Permissions" at the bottom. Let it run until it's complete. It only needs to be run once.
If that doesn't help, reboot with your Mac OS X Install CD in the drive, and immediately hold down the 'c' key and keep it held down. Soon, you should be presented with a window asking you to select a language for installation. Instead of selecting a language, select "Open Disk Utility" from one of the menus in the menubar (I think it's the File menu, but I could be wrong). When Disk Utility opens, select your hard drive, then click "Repair Disk" (not "Repair Permissions"). Let it run until it's complete. If it reports that it found errors on the drive, run it again and keep doing so until no errors are reported.