I'm really confused, do repeat courses get averaged or not?

You have to careful about using the term "repeated course" because some people have repeated a course more than once. Only the last attempt on a course is computed into your GPA but the grades for each attempt is still shown your application form.

Let's say you took Organic Chemistry 3 times. Let's assume you failed the course the first 2 times and received an A on the 3rd attempt. Your GPA would only include the last attempt or the A. However, your transcript or AACOMAS form would still show 2 F's for the first two times you took the class and an A for the last time you took the class course. So yes, your GPA could benefit greatly by repeating the course. However, DO schools would still see your original grades so it's not like they would never know you failed that particular course. You have to list how many times you repeated the course.

I have never heard of a particular school going outside of AACOMAS and applying their own policy of averaging all the grades as opposed to going by AACOMAS' rules. Maybe this true for Chicago but it's not true for AZCOM. I doubt Chicago does this. I'm sure whoever you were speaking with was confused or didn't clarify themselves well

 

I also contacted AACOMAS when I was filling out the application. As you found out, only the most recent grade will be used to calculate your GPA scores. The schools will still see the original courses and grades, but they are not used to re-calculate your GPA. In fact I don't think the schools have enough information to recalculate your GPA if they wanted to (they do not have the points per class). I can verify that only the most current classes count towards GPA by my own AACOMAS verified application.

There are several of us in the same boat. The most important thing is to ace all post-baccalaureate classes to prove to them that your new scores accurately reflect your academic abilities.