I am also experiencing the same problem. The issue is in the kernel extension, which, after the first use, makes the kernel believe that there is no Apple Remote anymore.

This is what I get after the first Front Row activation in system.log, if I try launching Front Row either from the remote or by launching "Front Row.app" from the terminal:

"FrontRow[357]: No Remote Present - Exiting".

Even quitting Remote Buddy and opening the Front Row application from the finder has the same effect.

Removing Remote Buddy's kernel extension solves the problem, and the Apple Remote starts working correctly again, albeit without the excellent Remote Buddy.

I hope this helps, 
Luca

PS: my setup: Intel Mac Mini, OS X 10.4.11, Remote Buddy 1.8.7.