Forensic Chick,
I have a similar problem with my application. I was an engineering major, and my engineering classes all count under AO. However, all 21 credits of calculus that I took (mostly C's) count in BMCP. So, I have a big discrepancy between the two. I also have 32 credits of post-bacc BMCP A's.
I wish I could tell you whether it's bad or not. I can tell you that I applied last year (with a pretty high MCAT) and haven't gotten in yet. None of the schools asked about the discrepancy though. I only applied to three schools (one AMCAS) so it's hard to say what is based on my grades, my situation, or my limited choices.
So, no answers, but lots of sympathy! I agree with tater tot that it can't hurt to take some post-bacc classes during this cycle. Then if you don't get in this year, it will slightly improve your BMCP for next year - and it will look good too.