Negrito:

The reason for the misbehaviour of your models lies in the fact that there seem to be different "dialects" of the OBJ-format description. Some programs add code in a "dialect" that is incompatible with the SH3D "dialect".

You will have to import your models in a program like Art of Illusion or Blender. There you can apply different textures to each part of your model(s). After doing that you export the model again in a format that SH3D can read.

Sometimes importing the model in AOI or Blender and saving/exporting it again is enough to correct a misbehaving model.

Hans