Sorry, I was having trouble imbedding the pics, so I've just linked the post to the url.

Pic 1 with correct lighting

Pic 2 with incorrect lighting

I've tested again with the model in the above pics.  The vertex count in the original is 3911, and the vertex count in the second pic is 2235.  No changes were made.  I simply imported the model and then exported it, with the drop in number coming after exporting.

On the other hand, I had another model I was working with in the same batch that had no changes whatsoever.  The other six are like this intrepid class ship though.  That makes me think it could be something with the model.  I can't speak for the nuts and bolts of the models themselves, though, as they belong to the SOA2 mod and I joined the team long after the models were set in place. 

It isn't visible in the pics above, but I've also noticed a great deal more effect from the reflective surfaces on the models, as well.  It's almost mirror like in some instances, to be honest.  There also seem to be a few area of the self-illumination map that aren't coming through, like the deflector underneath the saucer.

As I posted earlier, I've noticed the smoothing changes on all of the models I've worked with, and in some cases there have been some slight issues with the textures and lighting.  Only on a few instances has anything ever been as distracting as these bugs.  Again, any help is welcome.

I don't know if it happens when it's facing specifically away, but there is an angle where the black part lights up and the lit part goes black (or any degree of opposing changes in between).

Does the normal map texture have an alpha (duplicate of the red color channel of the normal map)? Just want to eliminate that because it was a common mistake in the early days of sins modding. It caused just what you posted, and/or "Black ship syndrome".

The SoA 2 intrepid was made in 2001 by the Homeworld SoA mod team (which i was a part of and had a hand in building the ships), and was not intended for a game like this. Homeworld used many "little" separate textures as opposed to the large single sheet textures sins uses. At the time we had to divide the mesh into many groups to UV map those little textures. Some models would have 40+ mini-textures. Thats how Homeworld 1 worked. I combined all of those little textures on to a single sheet, and re-UV mapped the model for sins. How it looks in sins depends on how "broken up" the model was to begin with. Which is why i planned on rebuilding most of the models themselves to eliminate those issues. Since i cant seem to weld any vertices, and smooth in XSI the way we can do it in max. The nasty texture seems are the end result, and they stand out most on the galaxy, defiant, and constitution models.

The 2nd immage remind me of Un welded verts after uvw and export.  Check if those areas have 2 verts not 1 on the model on the planes that show the errors.