ok, now you are sure it is a problem when saving your model to 3ds or when exporting the 3ds to cob.
It happened to me with old versions of lithunwrap: with the older versions when saving to cob all the model was faceted and it was impossible to change it, changing the material had no effect at all on how the model looked in truespace. I had to use intermediate file formats and to upgrade my version. It is strange btw that it happen to you only on specific faces on specific layers.
Anyway... knowing how good you are I'd tend to exclude geometry problems:)
Btw you may try to check if there are double verts or if the model is not solid in truespace. It may happen during format conversions, althought it is unlikely using 3ds.
edit: I suppose that in max it looks fine, right?
suggestions:
1-export with 3dexp
2-try to export the subobjects individually
3-try to use some intermediate formats (there may be problems with uvmaps, thought
4-convert back from pof to cob: the newest version tend to save the cob as completely smooth, and verify if the cob is ok this time
5-if you still have it and if it works with your model (if you don't have too many polys to make it crash) try to use the old pcs version that automatically smooth everything, and then convert back it to cob. If it crash, convert the subobjects individually. If you don't have it, I know that there are some guys here that still have it, not sure who, probably vasudan admiral
If nothing of the above will work, upload it somewhere and I'll give it a look