You probably didn't uninstall Remote Buddy's driver. You can find 
instructions on how to manually remove it in the FAQ.

It would be wrong to say, that Remote Buddy is causing a problem here, 
though, nor is it related to the end of the trial phase:

Right now, Plex built-in Apple Remote support makes some assumptions 
on HID system internals that can easily lead to it not reacting to 
Apple Remote events correctly - or at all. That's not particularly 
Remote Buddy's fault or the fault of its driver - which work correctly 
and in harmony with all other software supporting the Apple Remote 
direclty - including OS X, iAlertU, etc. It's a result of Plex' built- 
in support making these assumptions on the HID system internals.

Since this affects the user experience of Remote Buddy users, I've 
gotten in touch with the Plex team about this just yesterday and am 
currently writing up some sample code for them that should be of help 
to them in making their Apple Remote support rock-solid and more 
future-proof, as it is then no longer based on assumptions on HID 
system internals that are prone to be changed by Apple sooner or later 
as OS X evolves.

Best regards, 
Felix Schwarz