OP here. I had another experience with paid 'R' class being confused with an upgrade at the airport the other day, so thought I'd share...

I booked a discounted J ticket through AmEx Travel, which booked into 'R' class (while most of my EP upgrades have been clearing lately, this flight was down to just a couple of J seats when I booked, and I didn't feel like rolling the dice on an upgrade). I was connecting at DFW and my connecting flight was delayed. After standing around the gate area for a while, I noticed the flight crew come off the jetbridge and leave the gate area. A couple of minutes later, a delay due to a maintenance issue was announced.

I noticed another departing flight to my destination leaving about an hour and a half later, with one J seat still available, so I headed down the D concourse to the AC and went to the desk to request that I be protected on the next flight (with the FAs getting off the flight, I assumed it could be a lengthy delay).

At first, the AC agent told me he couldn't protect me on the flight. When I asked why, he said, "Oh, this is an upgraded ticket anyway since it's in 'R', so I can't put you in Business." He then said backing me up on another flight would cancel my original flight, which he wouldn't want to do either.

It took several minutes of discussion with him to convince him to look into the ticket further to confirm that I had paid for J, which was a bit embarrassing with at least 2-3 other passengers standing around who could overhear the conversation. He really seemed to have a hard time believing that, even though the flight was ticketed in 'R', it was a paid ticket. I also told him I've never had issues being protected in similar situations in the past.

He told me to wait while he checked, and after typing for several minutes (I can only imagine how many different screens he must have been going through to check -- seems like it must have been a fairly convoluted process), he finally agreed I was traveling on a paid ticket in 'R' class. He also then noted that, because I'm EP, he would be able to protect me and print a boarding pass for the last J seat on the next flight. He seemed nervous about the whole thing and said he would have to keep watching the original reservation to make sure the system wouldn't cancel me off the delayed flight.

Ultimately, the original delayed flight ended up departing just before the later protected flight, and I flew on my original reservation, so it all worked out in the end. I was disappointed, however, to have to deal with the 'R' class issue again. I really wish they had kept paid and upgraded fare classes separate, because AA's IT and their phone/AC agents seem to have ongoing difficulty distinguishing between the two types of tickets in the same fare class.