If you're using a Mighty Mouse try cleaning the wheel. Dirt and grime gets built up and the wheel won't scroll properly. This happened to me a few times and now I clean it regularly. For some reason, the down motion always stops working (or doing the side to side thing), never up or sideways. There are plenty of threads on Apple forums but here's one to get you going:
http://discussions.apple.com/thread....55121�
Hope it helps...
*Edit* sorry, if you're only having problems in one app and not system wide the above is useless. Should have read the original post better

ops: