Ok I have done this about 15 times today and my results are the same every single time.  I have no clue what else to do.  Lets do a step by step:

 

After checking 100x in modeling program to verify that every single edge is connected and welded - vertice and poly too...
I import boxers.obj in poser.  
I verify that boxers fit model in zero position.
I take boxers into setup room.
I load apollo bones.
I delete 3500 bones (ok not that many but after 15 tries it feels like it), leaving pelvis, hip, lthigh, rthigh, left shin, right shin and gen 1.
I go to group (still in set up room).  I click autogroup.  
It gives me groups for gen1, hip, lthigh, rthigh.  I adjust them.  
Now I've tried clicking weld groups and not clicking weld groups.  (even tried different tolerances)
Go back to pose room after making sure no pop up warning about unassigned polys.
I save to library.
Load apollo - reload boxers - conform to apollo:

Every single time without fail the boxers have had splits along every single group.

I'm pulling my hair out here - it is beyond frustrating to follow every single step to the T and still have this happen.

Any more clues?

I am:  aka Velocity3d