Now I can see the issue, it very tricky. The attraction property of the windows and borders, menu bars reserved space, the changes of the internal resolution of the game itself, etc. Can backwards the fullscreen exclusive mode to fullscreen windowed mode.
When this happens, it's necessary to reposition the emulator window without interacting with the borders of other windows/bars, in the worst case reconfigure to windowed mode in order to reconfigure fullscreen mode correctly. It's a pain in the ass.
The reason I can't reproduce the issue at first is because of my quirky setup ...borderless.
P.S: Make sure to have "Stretch with GDI" checked in the View > Video Output...
Edit:
P.S. 2: A quick fix could be forced prevention from stealing focus...