Below is an excerpt from this amcas manual:
http://www.aamc.org/students/amcas/amcas2009instructionmanual072808.pdf
"Repeat
Any course attempted more than once, unless the final grade initially
received was Withdrawal or Incomplete.
 A course entry must be made for each completed attempt of a
repeated course, even if any mention of enrollment in the course
has been removed from the transcript.

AMCAS includes all attempts of repeated courses in GPA
calculations, even if they are not included in the school's GPA
calculations.
 Do NOT select Repeat for courses designed to be repeated (e.g.,
Independent Study, Thesis, Chorus, etc). See Deferred Grade.
 If your school has an academic forgiveness policy and
subsequently replaces the original grade received with a special
transcript symbol the original grade must
be entered on your AMCAS application. If the original grade is
not entered AMCAS will return your application to you to enter
the original grade. Please note that this may cause you to miss
application deadlines.
 If you do not list all of your attempts in a given course, AMCAS
will initiate an investigation. "