Ok. I've used these together before and had no problems. I had MCA 5.2 installed along with The Undead 3.0. When I first loaded up my game, it said 'Missing Master: Morrowind Comes Alive.esm". That's strange, since I clearly saw the MCA.esm in Wrye Mash with a check next to it. Mlox told me there was an MCA/The Undead compatibility patch out there which replaced the 'More Enemies' .esp as well as the MCA.esm. After over writing, it now told me "Missing Master: MCA.esm". I then noticed there was a newer version of MCA (6.1), and I guess I assumed that this would fix the problem. It didn't. I'm not sure what i'm doing differently now then I did before when this worked fine. Anyone have any ideas?
Edit: I'm also using an .esp called "mca_playable_hnh" (heads and hairs) that I wasn't using before. I don't know if this has anything to do with this problem, but I thought I should mention it.