The scroll bar should function as expected. I would guess that perhaps your screen calibration is off, so that when you touch the screen where you think you're hitting the scroll bar, the iFly thinks you're touching off to the side or something and doesn't respond the way you expect it to. (This has happened to me...in fact, it happens quite frequently with my 720. I have gotten into the habit of recalibrating the screen every time I power it on the first time of the day.)
Try going through the screen calibration routine, and see if that solves your problem.
(One question: If you can't scroll to the bottom of a more-than-one-page flight plan...how did you ever manage to enter the flight plan in the first place? When I enter my plans sequentially from beginning to end, I need to constantly scroll to the bottom to add the next waypoint.)