I think the process was different for those who wanted it shipped vs in store pickup.I downloaded the Apple Store app and had my iphone ordered in 10 minutes!
I would hope this would all be resolved by the time you pick up your iphone and pay. I would let things settle down for a few days then look into it or call your local store and ask what's going on.
I would check and make sure there are not 2 orders out there somewhere. If one order had "claimed" your upgrade, it might have caused the second to come out at full price.
I woke up around 4AM ET (regular hours) and pre-ordered via my AT&T Premier business account for 2 iPhone 4 (32gb) - two separate credit card transactions - easy process completed in 10 minutes shipped to my house.
Note: White iPhone 4 currently unavailable for pre-order or in-store pickup for both Apple and AT&T. Reason: please ask Apple.
It took 10 hours to get my confirmation email from the Apple Store.
That's so weird because I live like 5 minutes away from my AT&T store and when I got home I had like 3 emails waiting for me already.
The white phones are in very short supply for launch.