When I applied, AMCAS screwed up my grades so bad, I'm lucky to have gotten into medical school at all.
Here's the story:
I started college at 16 and got my Associate's degree in 2000 when I graduated from HS (Running Start Program). I transfered and finished my degree at a university. I took a total of 5 years because I decided to pick up a couple of minors in addition to my major and emphasis.
AMCAS coded my entire Associate's degree as high school and then coded the rest of the time I spent in college as Freshman and Sophomore years. Basically, I was applied after my 4th year of college, but the med schools all thought I was a college junior.
I told AMCAS about the problem in August, they told me it was coded correctly. At my first interview in December (my state school was familiar with the program), the interviewers asked me when they would be receiving the grades for my junior and senior years of college. I contacted AMCAS again and they said they would work on it.
After arguing with AMCAS for months, they finally straightened out the problem on March 18 (a little late for most schools).
The end result: I applied to 10 schools with good stats. I was rejected presecondary from 5 because I didn't "meet the requirements" for those schools (they thought I was a junior). I was rejected by 3 schools post secondary and one post interview. At Wake, I was waitlisted until AMCAS fixed the problem. Ultimately, one acceptance was all I needed, but there was more stress and grief than necessary all because AMCAS screwed up.
The moral of the story is, it happens. Contact AMCAS right away and bug them until they fix it. It's your future on the line and I don't think they really give a care.