I happen to be one of them… I would have pre-ordered online from Apple if it weren’t for concerns about upgrade eligibility. I got to my local AT&T store and pre-ordered around noon EST on the 7th and I’m still waiting for my iPhone 4S to ship.
Update Oct 20 8:23 AM: My order is no-longer listed as back-ordered, however still pending shipment and my card has yet to be charged.
Update Oct 20 4:18 PM: My iPhone 4S has shipped! Will be here tomorrow via FedEx. 1 week late.

This MacRumors forum thread is full of unhappy day 1 (Oct 7th) AT&T iPhone 4S pre-orderers. There doesn’t seem to be any logical reason as to why one person has gotten their phone already and another’s is still back ordered. Some people are reporting finding phones in-stock at local stores and then having to fight with AT&T to cancel their pre-order to buy the phone in-store instead… AT&T seems to be favoring store walk-in inventory over fulfilling pre-orders, essentially punishing the most loyal customers.
With this being their 5th iPhone launch you’d think AT&T would have gotten the logistics right this time.
Last Time
Besides online pre-order servers crashing June 2010 for the iPhone 4 launch, I wasn’t aware of any real issues so long as you managed to pre-order before the end of the day. I didn’t even pre-order until the end of the day in-store because I couldn’t get an online pre-order to work, and still got my iPhone 4 on time.