I thi k the issue is materials I had, and possible MilkShape. It seems that, according to documentation, AppGameKit loads models using the lowest amount of meshes possible, and it seems to do this via materials. What I've found is a model with 3 meshes with no materials set as a .obj format loads with one mesh. If you set them with 3 different materials and save them (not UVs) then you get the 3 meshes. If two meshes share the same material, you get two meshes, one for each material. So it seems AppGameKit uses material data to decide how many meshes to have.
So the rule seems to be use a modelling program to set up materials....or use something better than MilkShape.