AACOMAS only takes into consideration the most recent grade for a class that you took more than once when calculating GPA. However, all classes and their grades show up on the AACOMAS application that the schools see. My GPA was 3.25 and my MCAT was 28 but I also had 4 years of spinal cord research and some letters from alumni and UMDNJ professors that I had worked with.
Here is my opinion; and you wont get the whole DO schools don't care about numbers, it's the whole person crap from me. Medical school is medical school, MD or DO. Everyone has to go through some sort of trial, some sort of adversity from time to time in their lives. Its how you rise above it or rise from being knocked down from it that counts. It's okay to have some bad grades if you went back and showed that you could do it after. But lets face it, a low GPA is a lot of bad grades because you have over 128 credits when you graduate. Even if you screw up a year due to some event (like I did) or just because you screwed up and then go back and work hard to fix it you can get that GPA up above a 3.0. Med school is not hard but its intense, expensive, and its fast paced, there is no time to get knocked down and not know how to get back up. I think med schools more than anything want to know that you can either a) stay on your feet, or b) pop back up quick enough. I guess what I am trying to say is that if you have to go back for a year and pick up that GPA, do some research, or whatever else med schools want to see on your application, then do it. The cold hard fact is that there are more applicants than seats and if you dont do it someone else will.
Once your numbers get to a decent enough level (lets say 3.0 and 25 with one or the other higher, to be very generous), other parts of your application can shine. Maybe you have some unique experience or talent that can bring diversity to your class, or maybe you can show through your writing what you are passionate about. My other point is that just like a person with a 4.0 and 45 MCAT but no passion or experience can get rejected, so can a person with a Nobel prize but a 2.0 and 18 MCAT.
Now, there are some schools that are number ****** and pass up great applicants or schools that have too lenient admission requirements and gobble up applicants as fast as they can, just like there are some poor performing applicants that get in and some great applicants that get passed up. There is luck and timing involved in the process as well.
Anyway, these are my opinions and I know for a fact they arent the consensus on these forums so take them as you will.