Regarding BA reservations disappaering, it happened to me before too. I had NRT-LHR with BA reserved in a PNR made by AA, however, didn't show up on BA's computer. Luckily, I noticed two days before departure when I called BA (I always "re-confirm" with the career because I do know s*it happens), called AA, and eventually had them talk to each other directly. Was told that it was a computer glitch, and it was finally sorted out by manually putting in the record at BA's end.

Sorry to hear about the not-clearing of the waitlist... Shouldn't happen...