BA systems definitely have a similar issue although it didn't keep me from booking. My itinerary includes ORD-EGE-ORD which are both flight AA 2185. Every email I have received from BA, including my initial confirmation with ticket numbers incorrectly states that I am going ORD-EGE, ORD-EGE.

When I pull the itinerary up on BA.com, the correct direction shows... so the same flight number probably messes things up here and there for various partner airlines.