petros--i responded to this in the other quarter system thread, but my undergrad school is on a quarter system and i had the same out-of-order problem. i called AMCAS three different times about this, and this problem is actually the reason why i started checking out this board for advice. based on what the ever-helpful people at AMCAS told me, i entered everything according to the instructions and left it looking incorrect (ie, winter quarter out of order) and submitted my app on the 24th, the first day i could submit (i'm an 'M').
to this day my app STILL hasn't been processed. my MCAT scores showed up the same time baylor21's did, and as i am a reapplicant, the year i previously applied has shown up next to the schools i am applying to for the second time. but NO progress on grade verification. you raise a very good point that i hadn't considered yet.
anyone else in the same boat?