If FPS is predicted to go over 60, Powder Toy will pause for a few milliseconds between frames. (Only a few to keep motion smooth, and because some of us have slower computers and don't need big pauses).
Perhaps there should be a while loop in there to account for computers that are far too fast ;-)
In older versions, there was no limit on how many frames were calculated and displayed, just an inaccurate limit on how often frames incremented the FPS counter. That limit gave a maximum of approximately 62 fps.
Edit: while loop now added in my github branch. 60 fps is only an approximate limit, so you might get a slightly higher maximum. But 91 or 100 fps is excessive... D: