I had a similar experience with BA in January. I had booked a Visit Europe Pass ticket on BA, CDG-LHR-CDG, in conjunction with AA travel from North America to CDG. At the BA desk at CDG I was told they could not access the AA record of the ticket, even though they could see my reservation, so I would have to buy a new one at the walk-up rate. The only way I could get the $120 round-trip Visit Europe fare would be to go to AA at the other end of CDG (Terminal 2 vs. Terminal 1). Since the plane was due to take off in about 40 minutes, this was not practical. I paid the $500.

AA gave me a voucher for the difference, so in the end I didn't lose, but it shouldn't have happened in a "seamless" alliance.