This is not new. Once you attempt to check in online via ANY means, you will not be able to complete any further seat changes or upgrade requests online or via phone reservations. Only airport agents have the power at that point.
In the old days, it was no problem...you simply called up your favorite AAngel at your hometown AC, and he or she took care of it for you. Nowadays, it has become more complicated, since most ACs are no longer reachable directly--you must go through the main Executive Center switchboard at ORD, at which point they will try to transfer you over to phone reservations agents who cannot do anything.
NB: The EXP Desk still has the power to call ticket counters, gate counters, AC front desks, etc on your behalf. But you have to have a VERY good reason (and a sympathetic, willing EXP Agent). The last time I did it, I was on an inbound longhaul international connection at DFW, connecting to the last LGA flight of the evening. I was running as fast as possible through the terminal and made it to the flight with about 30 seconds to spare before the door closed. I made the flight only because I had been on the phone with the EXP Desk as I ran, and the very kind agent was negotiating on my behalf with the DFW gate agent working the LGA flight!