I've been giving this a few shots, and have been able to recreate what I think is your problem (multiple blank maps on a plane - for me even the regular method of generating a map was blank).
The error was happening when the uv's borders were directly on the 0 or 1 coordinate boundary, MME/zbrush sees this as extending beyond the 0-1 boundary, and then reads it as multiple tiles according to marcus_civis (
here). Scaling the uvs in a tiny bit solved the problem for both generators, and created only 1 map for MME.
"You can check this by pressing Tool>Texture Map>New from UV Check. A UV problem will be shown as red."