I don’t know how one does it in Maya, but in 3ds Max I have to select all vertices and then click the Weld Selected SubObject button in the Unwrap UVW modifier. This welds all vertices with ones that overlap. Then it’s a matter of selecting each UV island one by one to make sure everything went smoothly. I run into the same problem with 3D Coat. For some reason the Unwrap UVW modifier in 3ds Max automatically breaks up my UV islands if the angle is above a certain threshold and I have to do the same method of welding to fix it.
I’m not sure my comment will help you, but from the sounds of it this is the problem you are having. I read another comment the other day by someone having trouble with ZBrush generated UV’s + normal maps when rendered in other apps. He felt unwelded UV’s were the problem because welding in another program would fix it. So if you know how to easily weld overlapping vertices (and only overlapping ones) in Maya, that should solve you problem. That is provided I understood it correctly of course lol.
Edit: Here is the link to the thread I mentioned.