Piggybacking on this because it's somewhat related - if I run desktop at 4k then play a teknoparrot game at "fullscreen" for example Transformers Human Alliance, the desktop automatically switches to a lower res, and the game goes full screen. Upon exiting the game the desktop switches back to 4k, but during that switch BB gets confused and hops on to the marquee.
I tried all shift handling settings, and turned display validation on/off with each setting. No improvement. Running BB 13.22 and the newest Third Screen plugin.
The only way I could get it stable was to run QRES first to set my desktop at a lower res, then QRES again on exit to restore 4k. Then BB was able to find the main monitor again. This option works but it's kinda janky to watch it happen - BB flashes a couple times before settling down. Also, I may have to set up additional apps for every TP game that runs at a lower res, which sucks.
All I can say is running a 4k high refresh monitor with BB, plus a marquee screen, plus many different emulators is TRICKY! QRES is really helpful but it gets really tedious when simple resolution settings break the whole setup.