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Windows Problem with FPS


I have a problem with my frame rate and I can't understand what's causing it...

When I run my game inside Game Maker everything is fine. I can even create a .exe file, run it and play without problems. BUT! When I close Game Maker and exit Steam and then run my .exe file again I get 20 FPS less than before. And if I start Game Maker again my FPS goes back up.

What is going on?

EDIT: My friend got 40 FPS on his computer too, even though the real fps was over 2000. So I told him to download Game Maker on Steam. He then ran Game Maker in the background and the FPS in the game went up to 60. This makes no sense!