Okay, I fixed it. To anyone else experiencing this:
It is obviously a bug in Bliz Art Tools, I don't think .mdx files are able to handle extremely small models (maybe the vertexes overlap horribly or something?) so when I deleted those animations and replaced them with animations where it goes under and above the ground, it fixed it.
Having small models also fucks up the unwrap. I tried exporting a normally sized model and a small model, the normal model had the unwrap as I made it, but the small model, with the same unwrap (atleast in Max 5), had a totally fucked up unwrap.
This is certainly strange.