Hi again,
I found a fix for my issue : it is indeed a common problem with Godot, and appeared since multi window was introduced.
Luckily, it can be fixed via an editor setting, that can be passed on command line : --single-window
Using this in Godot editor itself is not ideal, because it prevents embedding the game in the editor, but with pixelover I really don't see any difference, I don't think that multi-window is used by pixelover.
My recommendation would be to use single window by default in pixelover builds ;)
Hope that helps, thanks again for this great tool!