thanks for asking.

First of all, Remote Buddy can't cause this - it contains zero code 
that could affect the operation of the Apple Remote beyond it running 
(and even while it's doing that, it's completly passive - only 
listening for events).

Having said that, here's my best guess at what may be causing you 
problems:

From what you say, this sounds a lot like either your Mac is paired 
with a different(*) Apple Remote or your Apple Remote is deactivated 
in the System Preferences.

You can find options for both unpairing and re-activating your remote 
control at the foot of in the "Security" pane of the OS X System 
Preferences. Both options affect Apple's driver directly - and thus, 
in consequence - Remote Buddy as well.

Hope that helps and best luck, 
Felix

(*) It could, in fact, even be yours. You can increment the ID of 
your remote by keeping Play + Menu pressed for a couple of seconds. 
Which, in turn, makes it look like a different remote to your Mac.