What is happening here is that the Default Behaviour (which is pre- 
mapped to actions from the Audio & CD / DVD Behaviour) is 
automatically chosen because MC2 is no longer the front most 
application (the screen saver is now).

If you want your selected Behaviour to stick until you explicitely 
deactivate it - and no matter which application is active / front 
most - you have to turn on

"Manually activated Behaviours stay active until they are 
explicitely deactivated"

in

Preferences > General > Advanced…

It was the default once, but the concept of auto-switching and manual 
switching turned out to be confusing for too many.

Virtual Mouse & Co. make Remote Buddy API calls to ensure the 
"stickyness" of this selection. You can also achieve this through 
AppleScript for any other Behaviour.

Best regards, 
Felix