Update 6:
Fenomenas suggested me to re-create everything as simple as possible. I had my doubts that this would make any difference as the algorithm
I think the root of your problem is that the "vertical sync" isn't the same as that of the screen. This is the same problem that occurs when looking at a 24fps movie on a, say, 60hz screen. The updates won't perfectly match up (in your case 100/60) and when they hit a bigger jump it will look like a small jitter in movement.
This can be somewhat remedied by lowering your frame rate, anything above that of the screen is just waste of processing power anyway. It can't really be avoided entirely, although the newer wmodes for flash embedding might be a possible solution.