Lexor: I've checked some other things that were new in AP (new rules of Higher Magic skill, new skills of bowman / swordsman) but so far haven't found anything buggy.... hmm.... any ideas what to check?
I'm afraid i don't remember much from KB and AP. Still working on playing though them again. But so many things happen all the time [tropico4, dxhr, minecraft1.8, bloody new heating pipes being installed at my house..]
Is is possible, that since AP was based on KB's code, that GOG based their patch on a branch already 'infected' with AP changes? I mean, AB is like a "newer/better" version of KB, so it obviously fixes some issues still present in the original KB, it wouldn't really be a dumb idea, to base a patch on that code. That COULD explain some AP touches, like showflyingdead=2. Perhaps Your problem derives from that too.
I fear there is not much we can do. Perhaps KBAP's version numbering could tell us something? Unless they've reset them.
Does the build numbering reset when a new project is started on the same code?
[i'm not a programmer, i don't really know much about proper version numbering and such, forgive me if i'm throwing us off the right track here.]