That doesn't sound like what's happening - sounds like the system can't recognize that you have already paid. Simple solution is to call and ask for the seating change.

This sometimes happens to me when PNRs get split and my son (in E+ at ticketing) can't move with me. A call always rapidly (the one thing that seems to be quick to fix) resolves.

If there was only a price differential issue, you would see the ability to pick some other E+ seats for $0, others for some small additional amount and perhaps exit row for more still.