A few thoughts:

1) If you're using actions from the actual Plex Behaviour that comes with Remote Buddy: these haven't changed and Remote Buddy continues to send UDP packets like it also does for Boxee and XBMC. If Plex no longer handles/ignores these when in the background, this is a most likely a bug in Plex.

2) If you're using actions from the Virtual Remote to control Plex: again, these haven't changed in Remote Buddy and it'd appear that in this case Plex now turns off its Apple Remote support when in the background. This, actually, would be a good thing, because it'd match with how almost all other applications on the Mac use the Apple Remote.

Best regards, 
Felix Schwarz