Ouch, that's tough. Definitely give VMCAS a call (don't email; it's a waste of time and they take
forever to respond and even when they do, they usually just copy and paste an unhelpful answer from the FAQ).
To be honest, there's been a massive amount of issues with the Professional Transcript Entry service in general this cycle, along with everything else. I'd like to think that if your application has been complete and submitted since August 26th, the you SHOULD be in the clear. At the same time, though, you've already surpassed the turnaround date with what seems to be nary a word as to your status, which is very concerning to me. Like
@pinkpuppy9 said, contact them tomorrow (I doubt they're open today) and see if they can provide any sort of update. You're paying massive amounts of money to apply; you at least deserve to know where your application stands.
I hope that this all works out for you!

It'll be absolute bullcrap if it doesn't, though with how VMCAS has been this entire cycle, I can't say I'd be surprised... as sad as that is.