$1000 slam by Delta / Northwest -- Episode 1 of 2

This is the 2nd recent time where Delta/Northwest has cost me about $1,000.
I will describe the more recent experiece first so that I can document the resolution, or lack therof, in real time, through both the airline and my credit card provider, American Express.

1. Overview: I flew Detroit to Phoenix on Delta / Northwest in September 2009. I had a fully refundable coach fare. At check-in, I was tempted when offered to upgrade to first class with frequent flier miles. I was able to upgrade just the outbound flight for 5000 frequent flier miles.
2. Check-in: I was a little concerned when the kiosk asked me to insert a credit card. I even asked the agent who was running amongst check-in kiosks whether I was being charged. But a credit card is one option for the machine to just identify you at check-in, I had viewed the airline website under "Mileage Upgrades" which confirmed upgrades start at 5000 miles, the bottom line on the screen said "amount due $0.00", and the agent ( no doubt at least as concerned with the length of the line as my question) agreed it was a mileage upgrade, so I checked in and didn't think about it again for a couple weeks...
3. The Bill: I checked my American Express statement online and saw a charge for over $1,100 from Delta / Northwest. I immediately submitted a dispute. With the miniscule number of characters allotted to describe the scenario, I stated that I had not agreed to this charge and had supporting documentation. Needless to say, I was disappointed when American Express closed my dispute without even asking to see my documentation or hear my side of the story. This was because the airline's records showed I owed the money (well duh, that's why we had a dispute in the first place!).
4. Round 2: I emailed Am Ex to express my dissatisfaction. To their credit, they did agree to reopen the dispute to allow me to submit my side of the story (what a novel approach). I am in the process of putting this together now.
5. The Evidence: oh, by the way, the airline indicated I owe the extra grand not for the outbound upgrade but to exchange my return ticket. They have a new ticket number that I supposedly exchanged to during to initial check-in on September 21st. This is kind of odd, because first of all I apparently paid $1,100 to exchange my fully refundable fare for a non-refundable one in the same seat on the same flight. In addition to it failing that reasonable exhange test and their being less than zero quid pro quo (I was charged dearly for the inferior ticket), the boarding pass they printed for me on September 25th shows my original ticket number, not the "exchanged" ticket number they say replaced it days earlier.
6. The Expectation: I fully expect Delta / Northwest to extract any incremental $1 from me as a hub city customer, because they know they are largely the only game in town, so customer be damned. My first round prompt dismissal of dispute by Am Ex is likely a preview for their final resolution as well, but I'll be the first to commend them if it turns out any differently. They're supposed to protect against fraudulent charges and what else is a charge that wasn't agreed to?

I look forward to documenting the fate of this disputed transaction in real time. In the meantime, needless to say, I do not endorse any of the products above. I will have a more active recommendation at the conclusion of thus process.

Happy Flying!