the AMCAS application is supposed to change the calendar year of each term to the proper academic year. so it's totally correct that winter term of calendar year 1999 is being switched by the application to say 1998, because this is the winter term that fell in the academic year that started in 1998. fall term of calendar year 1998 would ALSO say academic year 1998, because it also is a part of the academic year that started in 1998. it's confusing, yes, but i imagine the software was programmed this way so that it was easier to match up the academic terms from the same school year, as all would be converted by the application to read the same academic year.
the topic has been thoroughly hacked to death here because for some of us (myself included) the application WAS NOT properly making this conversion for winter terms ONLY (but was working just fine for fall and spring terms). consequently, none of our winter terms were matching up with the proper fall and spring terms. but it sounds like it's working fine for you, so i wonder if the problem has been fixed?!?!
anyway, don't worry! the application is doing exactly what it is supposed to be doing! just be sure to enter the proper calendar year for every term.
good luck!