Thank you for letting me know.
Unfortunately issues with these kinds of hot keys are nearly going to boil down to Renpy itself and your machine. There's nothing in my code that I can change that is going to affect that.
For instance, I alt+tab in and out windows frequently when testing and never run into issues, but do sometimes hit a bit lag when using alt+enter to go between display modes. This happens not just for this game but all games I play (though it seems more likely to happen when going from full screen to windowed rather than the other way around).
If you're running into issues using hot keys, I recommend toggling the window in settings instead and see if your PC is able to handle that a little better.
~Steamberry