This happened to me, too. So frustrating. I was on hold for 10 minutes with Apple before I got one of the employees there who clearly has no idea what's going on. First, even after I told her what my Reserved confirmation said (to pick up at my local store, an hour away), she was trying to tell me I have to pick up at AT&T and when I asked her about the price, she told me that AT&T sets the prices, so I have to check with them, although AT&T already told me I'm eligible for the upgrade for $299. It's so frustrating to be jerked around so much between Apple & AT&T with their online ordering and then to get people who have no idea what's going on from Apple not able to clarify ANYTHING for me.
She also told me that the store doesn't open until 10am on that day although the email says 7am. I need to call the store, I guess.
I have a reservation. I've not upgraded my phone through AT&T since I got my 3G when it came out (maybe two years ago now?), am eligible for the max upgrade AND my confirmation says it will cost me $699. That's all I know.