Well polygons can consist of more than 3 corner vertices, and when that model is converted to something that doesn't really support multi-triangle faces (.scms for example), they will be broken down to triangles according to the face triangulation (they all still consist of sub-triangles after all). So non planar faces should be no problem.
Think you could help fix it Kirv? Or do you use Blender? XD
Blender could import the .obj and export an SCM for you to use. Of course, OBJ files can't store bones, so he'd have to rebone the whole model, assuming there were any to begin with.