One suggestion when you call in is to ask them to verify the e-ticket against the itinerary ... sometimes the itinerary will change and the e-ticket hasn't been updated correctly. This could be what is causing the issue on the CO side, esp if it is a 016, UA ticket. The other thing you can do is to look at the ticket e-receipt (although it is dumbed down) and see if the appropriate segments are represented on the receipt.

G'Luck!