At last a post to which I can reply. I had a PhD before going to medical school. I made sure that information was in my file (I don't know about the AF, but the Army has your file accessable online so that you can ensure the proper info is there) by having transcripts sent to the HPSP office. Like the previous poster mentioned during the FYGME application process in your 4th year you receive a letter (or email) stating that you should ensure all the information is in place. Since I already did that during the HPSP application phase, there was no issue and I received an additional 4 years of constructive service credit.
What is constructive service credit, you ask? Well, it is time for which you receive credit toward promotion. NOT toward retirement and NOT toward pay. Essentially I am starting residency with "4 years" under my belt as a captain, but getting paid the same as the rest of the interns. In the Army there is a 6 year promotion scale where after 6 years in captain one is promoted to major, 6 years as major to lt. col. So I have 4 already and will be eligible to be promoted to major in 2 years.
Does this make sense?
G