I took your advice and installed serialScroll. it's not live as of this moment (hopefully today though!), but I can tell I will like it better. And in the process of updating my page, I think I stumbled upon the answer to my problem...
My page has 2 continue buttons (actually more than that), one outside the scrollable region, and one inside (one per section). I was using position:relative on the inner continue buttons (to solve another issue), and IE got all flaky rendering those buttons, because I hadn't set the parent element (the LI) to position:relative. So I went ahead and did that to the LI, and it killed the scrolling effect! In this case, my solution is to not use position:relative on the LIs or any elements therein. I've spent too much time on this to test my theory on the old pages, but I bet it is something along those lines. Anyway, Thanks Ariel for your help and for your wonderful plugins!