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Automatic switching is independent of particular applications - including system applications like Finder, iCal & co. If it wouldn't treat all applications equal, people who want to create and use a Behaviour for the Finder (I personally know of some) would not be able to do so.
So, with automatic switching, the Behaviour to be used is *always* re-determined whenever the active application changes (which - as said - of course also includes switches to system applications like Finder, iCal & co).
This is what happens whenever the active application changes:
1) Remote Buddy checks whether it has a Behaviour that can control the currently active application. If it finds one, it is used.
2) When none could be found, Remote Buddy asks the Behaviours whether they are capable of controlling any of the running background applications. If several controllable applications are running, the application state is often taken into account to pick a Behaviour. If a Behaviour that can control a background application is found, it is used. Examples for Behaviours that can control apps in the background are - among others - the Behaviours for iTunes and DVD Player. An example for application state being taken into account: if both iTunes and DVD Player run at the same time, Remote Buddy will control DVD Player if a DVD is in a drive - and control iTunes otherwise.
3) If no Behaviour could be found in 1+2, the "Default Behaviour" is used.
What Behaviour is being displayed as being the Active Behaviour in the RB pull-down menu when you want to control Plex in the background?
Best regards,
Felix Schwarz