These are alternate bone assignment problems. The top half has some secondary bone weighting to bones below the waist, and vice versa, and the rendering engine stretches the skin to spread between them.
Since what you see now doesn't support the multiple bone assignments easily, you're having this problem.
The neck problem disappears on it's own, for the same reason (the vertices that make "ring around the collar" are split between the neck and head for bone assignments). With the way you get only default gloabl values for skin weights in BodyChop, the weighting to the head is too small to get the vertices into the places that Maxis designed them to be.
<* Wes *>

The simple cure is actually to alter the alpha-map.

You probably never bothered with them Wes, since they are a part of the texture rather than a part of the mesh information.

I also discovered early-on that some of the Maxis skins have faulty alpha maps to start with if you examine them closely.

The alpha map shows the game where to put your texture on the mesh (the white area), and where to put the texture from the "skintone" image (the black area).

I have never noticed this problem because the first thing I do after making a mesh is to use LithUnwrap to make a uv_map.

I then use this to make my alpha mask, or alter the Maxis alpha map as the case may be.

I always go a few pixels outside the areas indicated by the uv_map at the sides to be sure.

Then when I make my skins I also make the texture areas a few pixels beyond this "alpha" area.

Ah, that explains it Dr. Pixel. It so happens that the Maxis meshes that I have edited so far 1) had the alpha map extend past the uv map's edges and 2) had the clothing pattern extend past the uv map's edges, a generous amount usually - that seems to have been the texturing technique of choice for many of the clothing designers, and now we know why - so that any irregularities are handled.

That said, I have noticed (just skinning, not even modifying a mesh) that occasionally the Maxis alphas are just off, sometimes they don't meet correctly at the shoulders, so even if I'm just doing a recolor, I end up really looking carefully at how things look and adjusting the alpha.

Wow, I thought I had lost all ability to mesh yesterday when trying to do something based on a NL mesh. I spent 10+ hours working on one mesh, 8 of it trying to get it back in the game!
I'll just await the new plug-ins eagerly with everyone else. Thanks Wes H for working so hard.