I share your concern. I dropped off about 30 books at SDCC, over two weeks ago now. I had done the online submission and put all the book in proper order. The Express Drop Off took half an hour until I got the front of the line. The person helping me checked the books, didn't give me any kind of receipt. But okay, there was a barcode on the paperwork I had printed out, and I assume they'd scan that at the check-in, so the books would at least show in the system, even if they hadn't arrived in FLA yet.
Still nothing showing in my account; it says I haven't submitted anything in eight months. I sent message via the site form earlier this week, no response. Luckily I took a pic of the person who took my box of books, but I expect at least some reply and the silence is very, very concerning.