[Edi]

The misbreds have a special flag that makes them require undead leadership. It's working as it should be. Otherwise they would be too easy to recruit in massive hordes and just rush the opposition before they could do anything.

The vanishing prophet issue is in the shortlist as "BHV Unable to Get New Prophet", though that one is related to prophet dying of late winter disease. Do you remember if your prophet died in late winter? If he did, it may be a manifestation of the same bug. But I recommend doing as NT Jedi suggested and checking the commander orders for "Become Prophet" in case you missed the message.