From what I understand, residencies that are dual AOA and AMA allow you to go through the D.O. match with their residency first. If you don't match by February (day that AOA announces), then you get filtered into the M.D. side of things and are put in the pool with other M.D.s. If you do match on the D.O. side of one of the residencies, then you are automatically taken out of the M.D. obviously.
When you say low board scores, are we talking above or below 500? And did you take the USMLE? That sound like you are doing great if you have most of your programs inviting you to interview. Best of luck.