thanks for asking.

Remote Buddy does not alter the Behaviour of the Apple Remote in any 
way beyond the time it is running. When it is running, it makes sure 
Apple's rcd.app (a small background app that executes AppleScript 
snippets for every press on the Apple Remote) does not get any of the 
Apple Remote's input. When you quit it, it releases the lock on the 
remote‘s signals, so the system returns to normal and will behave 
exactly as if you had never run Remote Buddy before.

If Remote Buddy in not running, your Mac will *always* bring up Front 
Row when you press the Menu button. That's the way Apple designed it.

For your reference: http://docs.info.apple.com/article.html? 
artnum=302504

Best regards, 
Felix