Ok, so I've run across a problem, that I'm sure is an easy fix, but I'm sort of shooting at the dark and thought I'd post a question here.
I created a model in Zbrush, semi hires, only 4 subds worth(around 1.4 mil). I then exported obj without groups and imported into 3DCoat. I redid the topo, uvs and baked it. I then created a new scene in TopoGun placing the appropriate models into their folders that TopoGun created. I generated the maps, diffuse, ao, etc. I then opened the obj in Maya, and the textures are weird in some areas.
I thought the polypainted texture would have been fine. Nothing change as far as the verts go, so it's weird that the texture no longer matches the model exactly.