Oh, I remember the frustration ALL TOO WELL.
AMCAS said I was missing a transcript - which was completely bogus. I went to 3 undergrad colleges in total. One transcript had a reference of another school - which turned out to be a seminary class that gave me 1/2 a credit for religion at that school - but wouldn't typically be considered college credit anywhere else. AMCAS wouldn't even look at my application again until they got an official transcript - which this seminary didn't even offer - AND of course, it was summer - and everyone from that place was gone. Luckily, with some digging, I found the secretary - and I explained the whole situation about medical school, timelines, and my stress level. What a nice lady, she got a hold of the director, and they sent in a nice certified letter explaining all this to AMCAS and well after a month after submission, my application was finally verified...
Not sure how it affected my interviews - I had an incredible season. Good luck, everyone!