I use Remote Buddy express to control eyeTV and switch to Plex/ Xbmc for movies etc, but since a recent update the remote buddy express program seems to resetting back to default behavior. This happens when exiting Plex to restore eyeTV (always running in the background, muted), or when left on eyeTV for prolonged periods and often requires me to activate eyeTV behavior a few times before it properly activates..

Just wondering if anybody else is experiencing the same issues? 

Remote Buddy will choose the active Behaviour based on what application OS X reports to be the active application.

That is not always the application whose name you can read in the menu bar. Background/Helper applications running as "UI Element" can become the active application without OS X updating the menu bar or indicating this change visually.

Since the code that selects Behaviours has not been touched for years, chances are you've installed some software in the meantime that runs as "UI Element" and becomes the active application reported by OS X at the time you experience this issue.

If that active "UI element" app is not supported by a Remote Buddy Behaviour, Remote Buddy will pick the "Default Behaviour" since the active app is unknown to it.