Can’t replicate this behavior, also no changes to the desktop viewer since six months or so.
Multiple monitors may indeed cause issues, especially if connected to different GPUs, but since you already checked that, there’s not much left I could suggest in that regard. One thing you could try is to call the .exe with the -output parameter to select a specific monitor, e.g. vorpDesktop.exe -output 0 or vorpDesktop.exe -output all.
You can add command line parameters in the properties window of Windows shortcuts.