Apple Remote and Basic iTunes Control Loss

Earlier today I noticed that my Apple Remote had lost all capability to control iTunes while in the normal desktop of OS X. All other buttons did something but the three dedicated iTunes controller buttons had lost all ability to do anything in the main desktop mode of OS X (not Front Row or any other full-screen app in the OS). I know that the rcd.app was recieving the signal because of its slight jumps in CPU power when I press one of those three buttons on the remote. I tried quitting the rcd.app and the Dock.app and neither worked. In the end the fix I found was to logout and back in again.