Do you own more than one Apple Remote? If yes, chances are that you 
have paired a different Apple Remote with your Mac than the remote 
you're currently using.

To exclude this possibility, please unpair your remote and, if that 
doesn't solve the problem perform a reboot and also go through 
FAQ015E0222 "Remote Buddy does no longer react to button presses on 
the remote.", which lists further error sources like f.ex. a disabled 
infrared receiver in System Preferences > Security, which could also 
be the cause for the problem at hand.

Best regards, 
Felix Schwarz