Quote -
(B) If we export from Poser with [ ]include body part names and [x]weld, then the figure stays as a whole, but on saving, hexagon removes some of the vertices and adds a DEFAULT group, my main theory is that they are unused in the polygons because of [x] weld.

The welded mesh would have fewer vertices than the unwelded one. Does your program require one to work on the unwelded mesh? That would be quite limiting. Or does Hexagon also remove vertices that weren't originally welded?

I don't have Hexagon, but now I'm wondering how I would fare with my usual Wings3D workflow. The settings you mention under (B) are exactly what I'm using. Since I'm currently working on the final (hopefully, sigh!) JCMs for Antonia, I wouldn't mind giving your program a spin, if you're interested.

-- I'm not mad at you, just Westphalian.