I have exactly same problem when i open my published RemoteApp and then minimize on my monitor 2 and after this maximize, it maximizes on my monitor 1 which i dont want, it even is unresponsive after this monitor change.
I edited my rdp shortcut and add "selectedmonitors:s:1" - 1 is my second monitor. Monitor count start from 0.
Now is working ok. minimize/maximize on same monitor.
I read this things on hanselman com blog when you want read more about this or just search on google "rdp selectedmonitors"