I really don't think it matters that I worked in the highest subd resolution. Being able to go back and forth between different subd levels and have the changes transferred is such a core feature of ZBrush. It would be so much more of a pain in the ass if I had to worry about what the mesh looked like at each level.

Thanks for your help; I guess I'll keep looking at the zbrush export settings, or maybe maya doesnt know how to interpret/display the map correctly.