Yup- for AMCAS, both count- but I made sure to mention that my science GPA looks a lot worse due to that fact, and that there were a couple courses I trounced the second time around (no excuse not to). Also, be sure to get a good upward GPA trend, and try to ace the next course (if it's a sequence) or perhaps consider taking another higher level class in the area to show you can master the material (but only if you'll do well).