Not sure if this was a OW problem, or an IB problem...

Had these flights:
FCO-MAD IB3613 1215-1450 TUE18OCT
MAD-LHR BA0465 1720-1840 TUE18OCT
LHR-DXB BA0109 2140-0730+1 TUE18OCT *stop*
DXB-LHR BA0106 0155-0620 THU20OCT

I'm currently on a DONE3. FCO-MAD-LHR are the end of one coupon of the eticket, LHR-DXB-LHR are on the next. When I checked in this morning at FCO, the agent asked if LHR was my destination. I said, no, DXB is. DXB didn't show on her system until she looked ahead at the next coupon. She then tried to add that sector to the check in process. The boarding passes came out with little trouble. The bag tag however was a different story.
Whenever she tried to add anything more then MAD, the system tossed out "unable". About 20 attempts, several phone calls and 3 or 4 different ways of trying to process it, it kept throwing out "unable". Meanwhile, it's tossed out a boarding pass for DXB-LHR (which she was shocked about given when the flight was). In the end we could only get the bag to MAD and I had to collect it and hand it over to BA myself and she called ahead to get MAD to work out the problem while I was in the air. The agent in MAD had no idea how it could have happened.