Actually, this is pretty easy with Girder as long as the Theater View windows have different names.
My scenario is for multi-zone music (it doesn't work for video since you need the primary display). I have two video cards in my server allowing for 4 simultaneous outputs/displays. Each display is in a different room showing Theater View for a different zone and has an IR/RF remote control. I then configure Girder with my IR receiver to respond to the different remotes and send navigation commands to the appropriate Theater View window.
Ahhh.... I see. That must be a pretty darn nice setup (though I'd want to use it for Video too).
That's just not the way I'd personally accomplish the goal, but I always have a pile of unused motherboards, CPUs, RAM, and accessories in my basement office at any given moment... So my solution would be to build a PC for each room, each running it's own copy of MC, connected to a central file share and library share. Your way probably works too (and certainly is lower power), but you have weird issues like this.
In fact, that
is my solution. I have a Windows box in 4 rooms of my house, plus a laptop. One day, I'd like to get one for in the bathroom.
Since I believe MC stores it's instance zone settings in the registry, I don't know that there is any easy way for them to modify this behavior for your needs. Have you tried pointing the different instances at different libraries (clones)? Perhaps the current zone is stored in the Library, as opposed to the registry... I doubt it, but it's worth a go.