I was already using only a normal mouse yesterday because the 3D mouse was my first suspect. Now I got the problem resolved by also shutting down the 3D mouse software that was still running in the background.
I think you should look into this and figure out if the game takes any commands from the possible game controller in addition to the arrow keys and middle mouse button as the problem appeared with a steering wheel too.
Edit: sorry, page refreshed and I put this on the wrong comment
Don't know if you’ve found it yet, but I encountered this bug also and it seemed to be when going to the level select menu after solving the level, and not continuing to the next level, but I couldn't test it fully as I already had 3 stars.
The level doesn't need to be redone though, you just go back to the main menu then then back to level select and it shows your stars.