Bruh! I'm not sure if you all fixed this or not; I came in search of an answer because I too am experiencing this issue: it seems as if the full screen mode still behaves as if there is a bar at the top like in windowed mode. Clicking the area at the top will cause the focus to shift to the window behind the engine window which minimizes the engine window, but I noticed that when I switch back to the engine window, the problem seemed to be solved. This got me thinking and I tried something... I initialized my video like this:
Code:
video_mode = 12;
video_screen = 1;

Then, I used video switch to change the engine to windowed mode and back to full screen mode:
Code:
video_switch(0,0,2);
video_switch(0,0,1);

This seems to solve the issue, at least for my purposes. Anyone experiencing this issue should try this :3

Making dreams come true... And being erroneously accused of software piracy by Conitec in the process.