Not sure about that one Rezman. Usually the mouse wheel is an all-on or all-off kinda thing. In other words, if it's working on the site there's no obvious reason why it should stop working in your browser.
The only issue I've had with my scroller is when I used the Safari browser (was inoperative in-game like you described above). I would recommend switching to a different browser just to test the wheel out. If the same problem exists in a different browser I might try re-installing my flash, but I'm honestly not sure how that would solve the problem.
Good Luck and let me know what you did to get it sorted out.