Hard question to answer over the message board. Contact some DMEs in the specific residencies that you are interested in and ask them. But here is brief answer:
It depends on the residency. There are some ACGME residencies that require you to do a preliminary or transitional year. For example, Dermatology, Ophthalmology, Radiology, Anesthesiology, some Emergency Medicine programs will all require you do a preliminary year and then start your residency as a PGY-II.
Now some of these programs will count your AOA internship as your PGY-I (i.e. most anesthesiology programs will). However, the rest will require you to complete your PGY-I at an ACGME approved program.
If you have done your AOA internship and the program will not count that as your PGY-I, you will have to repeat your PGY-I again at an ACGME program. This creates some problems. Namely, you will add one year to your post-graduate training. Also, if the program decides to take you, they will only get half funding from the government for your last year of residency since you have taken an extra year to complete their residency program. Some programs might not take you for this reason.....