I guess the problem is that, when you pay for something, you only get issued a receipt once. The system should be able to handle issuing a duplicate receipt though.
The worrying thing from my perspective is that, by 2007 if IATA have their way, all carriers will be issuing interline etickets. If BA have these kind of problems then can anyone imagine the kind of issues someone connecting to BA at DME from Transaero or a regional Russian carrier is likely to have, with an eticket issued on the non-BA carrier?