I take that back... According to the newly updated FAQs on the AACPMAS site:
Q: If I have taken a course more than once, does AACPMAS take the higher grade?
A: AACPMAS will take the most recent grade received in a repeated course whether it is higher or lower than the first time it was taken. If you have a repeated course, enter the first grade in the College Courses Completed but leave the hours as zero. Enter the hours and grade for the course that was taken most recently to replace the repeated course. During the Transcript Review process, indicate that you have repeated a course, and mark the final attempts of any repeated courses as such.