Honestly, I'd be pretty worried; even if you got all of your secondaries in before the MCAT, they're not even going to look at your app until you get the MCAT. Being complete in late September is really getting on the late side of things.
I mean, there's not much you can do about it now, so definitely get those secondaries in so you can at least be done asap... just do your best to play the application game as well as possible from here on out!