What you describe sounds as if you have selected the "Expose"- 
Behaviour at

Remote Buddy Preferences > General > Advanced.. > "Activate Behaviour 
at start"

Setting that option back to the default setting of "None 
(recommended)" will bring back Remote Buddy's standard behaviour.

Remote Buddy can’t and won't affect what your remote control is doing 
at times where Remote Buddy is not running, though. Remote Buddy needs 
to be running in order to have any effect on what actions are 
triggered by your remote control.

If you experience unexpected behaviour of your remote when Remote 
Buddy is not running, you may want to check Activity Monitor for other 
remote control software or their remains (I know of at least one 
remote control software that offers an uninstall routine that does not 
work under at least Leopard).

Best regards, 
Felix Schwarz