Ah, I fixed it! It was a problem with the Mudbox settings when importing the new UVs. You can choose to assign it to the nearest vertex, or by vertex ID. When I was using vertex ID, it was for some reason deleting vertices, or not importing them properly. When using nearest vertex, it matched them exactly.
Hi PogoP, Thanks for tihs. I spent 3 days trying to work out this problem and your solution worked. I can't understand why VertexID doesn't work. I mean I exported an obj from level 0 in mudbox. Created my uvs in max. Imported uvs to level 0 using vertex ID and my painting kept messing up, until I found this forum. Thanks…