This happened to me and a colleague a few weeks ago as well, also with a shorthaul sector that had been the final one of a longhaul booking which had a 40 day stopover in London.

I can only guess that somehow the logic in the BA IT system falls over for these long stopovers, and there's some mismatch in the origin/desination information.

Funnily enough though, when I asked at checkin, the agent said it was because the system had somehow linked the outbound shorthaul sector to an inbound shorthaul on a different PNR (a redemption, in fact) that I'd done the previous day. The only common factor between the two was my Exec Club number. But if this actually was the case (and clearly since FLY was telling the checkin staff about my unrelated inbound flight, it was information that FLY decided was pertinent), then maybe it's an issue where someone takes another set of flights during one of those long stopovers, and that somehow corrupts the APIS record?