I also have had this problem from time to time. It is sparatic, but on occassion, remote buddy will open its window, but after I select a behaviour it will launch it, say Front Row, but when I click on a command on the remote the computer just beeps at me, no matter what command I push. So if I quit Remote Buddy and then restart it fixes the issue. I have even had this happen after it has been working fine and then it sudden will do it.

I can say I never had this happen until I upgraded to Preview 5.

It seems to be some kind of random bug.