In windowed mode on lower resolutions, the game sorta alternates between normal speed and running twice as fast. I'm using an 8 core i7 at 3.7GHZ.
This was once reported before as issue #100. I still can't reproduce the issue on any of my systems. My Windows computer is a Core 2 Duo 2.2GHz so it could be something that only manifests with faster cores.
If you turn on the fps display (Tab+D) does the game go to 140fps when it speeds up? Is it possible to get this happening in a video (even if it's a camera pointed at the screen)?
Looking at the function which keeps the game time, I don't see off hand what could cause it to go wrong, but obviously it must. Nevertheless there are more precise ways to do timing, which may increase performance.