Hi mbkatz, I think I had the same problem. What you need to do is specify that semester as "spring semester 2000," because AMCAS recognizes it as "second semester of the academic school year 2000." I know, it's confusing as hell...I guess they wanted to keep the semesters of the same academic year together in order to calculate grades by frosh, soph, junior, senior.
I only happened upon this fact because I skipped a fall semester during college. When I tried to add my preceding spring semester, it kept kicking me to the next school year!
Hope this helped. Good luck!