Tried to check-in simple HELTLL flt, my booking had my OWE BA number on it, but at check-in it was changed to my AY+ (Basic) number and was not able to change it.. resulting in "boarding pass cannot be issued due to unpaid seats".

Called AY, answered in less than a minute, said would call me back, did so within 5 minutes and everything was cleared and was able to do the check-in.
System glitches seem to be persistent, but phone service great!