Like it says on the tin.

It has my mod in place, but I didn't do anything with necromancers or zombies, I made dorfs build towns since fortresses were laggy and not as fun as towns, but I don't see how that could have caused this.

You're standing right where the zombies are, you've got syndromes on which make undead ignore you, you can just watch the merchants beat them down or help, when you travel away and back or wait/return they'll be back.