Ummm, only thing I can think of is maybe you have vsync force disabled on your GPU drivers? I'm not sure, but GameMaker may rely on that for frame timing.
Otherwise it would mean that your OS level timer is wrong, but that comes directly from your mobo so I don't see how that could ever happen.
Thank you, but I don't think that's it.
I have many GM games and I haven't experienced that issue with any of them...
But the issue starts at random and reverts back to normal after I restart BSF a few times, so it's just a minor annoyance and not a big deal.