This is now the second time I'm dealing with a situation like this. I am right now on hold (at the 53 minute mark on the call) with CO trying to resolve this.

I booked a MR trip to go AUS-IAH-MCO-EWR-SEA (then UA back to AUS on a seperate ticket) a few weeks back. About a week later, I checked the reservation and saw the upgrade options thing, and saw something to the effect of "upgrade now for $294". I thought to myself "damn, that's an awesome deal!" and booked it. The new reservation and receipt showed that it had booked me in Z class from AUS-MCO-EWR, and ZE (M-base) from EWR to SEA. I was pretty pleased with this.

Fast forward to today when I try to check in. No luck. I call reservations and they tell me they can't figure out why the ticket is out of sync, but know it's because of the upgrade I did. They transfer me to the electronic help desk, who tells me that I owe them appx. $1400 (plus a change fee!) if I want to stay in F. They're now in the process of bringing me back to my original ticket in Y to re-sync the ticket.

If this was another business, I'd be taking them to court for services not rendered! How does this nonsense happen - FOR A SECOND TIME! (the first time, they were 'nice enough' to waive the change fee to the F ticket)...

A good reason to make and store screen-shots of reservations, transaction pages, etc.

Woooooow. That's a huge mess up. Sorry man

Did you ever get a new confirmation email after confirming the upgrade? If not, that's a huge red flag that something didn't work right (at least that's been my experience...).