Are you within the hours window for that specific flight? I'm FO so I have to be within 24 hours. When Flt 1 in <24 hr I can check in, but if Flt 2 is say 25 hours out, I'll get that error trying to change seats on the 2nd flight (even though I'm checked in). The call reps don't appear to be familiar with this situation, and it's not really an error per se, just an incompletely documented function of the system.