You guys are fine.
Suppose you take a summer course between your 98-99 school year and your 99-00 school year. That course will be listed as 1999 (so, it goes w/ the academic year subsequent, NOT PREVIOUS). In addition, all the courses you take in 99-00 will be listed as 1999, even if the calendar year was 2000 towards winter and/or spring. Got it?
This is just so all the classes you took fresh, soph, jun, and sen years will each have their own year (which accounts for the summer session prior to that academic year too).
As long as your calendar year was correct, the changes AMCAS automatically makes are what it's supposed to do.
**NOTE: If you are on the quarter system, a winter quarter course (for example during 98-99) should have a calendar year of 98, EVEN IF it may have started in 99. Weird quirk, I know.
Hope this helps and didn't confuse people further. Take a look at the instruction book AMCAS has online...it really helped me to have a hard copy in my hands while I applied.