Yeah same deal in 3d max, because that's how vertex normals shade polygons, it won't be visible when your texture is 100% lit like in modview. Try this when compiling in assimilite:
Double click on humanoid, it should open a window with build parameters, there's smooth all surfaces and remove duplicate verts from mesh during compile, try one box, then the other and both to see if it makes a difference. I doubt it will work, but worth a shot.
The only alternate solution would be to weld back the lower body to the torso then create a dummy "hips" object (a simple triangle) hide it inside the character and re-do the hierarchy.
If you don't want to go that route, you could probably use a shader to tell the engine to use your texture as 100% diffuse, i don't remember what the code looks like from memory, but i could probably find it.