Somebody has got to have some answers, but I'll try to add a little till someone more knowledgeable jumps in.
I beleive that with AAMCAS, the new grades after retaking some classes gets averaged into one. So lets say you had a C in O Chem. And you retake it and get an A. Well I think it gets turned into a B on AAMCAS.
With AACOMAS, if the second time you get an A, then your reported grade is an A - hence you have a higher GPA with the AACOMAS system when retaking classes - but if when you retake, and you fail O chem, then your new grade is an F. 😱 So with AACOMAS make sure you do well the second time around.