There are still a few "traps" that you can tap into, though. Did you, 
for example, pair the Apple Remote with your Mac? While the pairing is 
usually enforced regardless of whether Remote Buddy is running or not, 
this is not necessarily the case when using the multiple remotes mode 
of Remote Buddy. In that mode, Remote Buddy allows presses from 
different remotes, while, when Remote Buddy is not running, the 
pairing to a single remote is effective.

The same also applies if you disabled the Apple IR Receiver in your 
System Preferences. Both pairing and disabling of the Apple Remote is 
configured at System Preferences > Security.

Please be sure to also take a look at the FAQ entry FAQ015E0222 for 
more ideas and information.

Best regards, 
Felix Schwarz