1. Did the original file exported from Maya in FBX format (or OBJ?) At first I exported in FBX format. Later I tried OBJ but I'm working in Z-up and so Unfold3D didn't adjust.
2. Did you create/delete/rename some UV sets in Unfold3D? or did you simply edit them? I did both, I was trying to make lightmap UVs for a bake so my FBX had its default UV set and I added a second lightmap UV set in unfold3D.