I had the exact same problem, although wandering out to the town gate and back again seemed to cure the NPC side of it. I still can't talk to Madora though...but I haven't tried heading to the lighthouse yet which I'm assuming will clear it.
Went to lighthouse already and entered lower floor, both ghosts are present but there is no dialogue option. I think I'm fubared!
I'll try exiting/entering city. If that doesn't work I'll have to reload save just before locked door and fight naties all over again. Oh well....
