I just downloaded the copy I uploaded, to make sure that if the problem is with the ship, I would have the best chances of getting the same results.
For all versions of the ship, I couldn't get the same errors you were getting on your end. However, the modviewer was reacting a tad on the slow side, but that might have to be due to the polys and the large number of materials the ship has. I've never done a kitbash this large, so I have no idea what effect that would ultimately have on modviewer on certain systems.
Have you tried the ships out in game yet? I know you don't have SFC3, but does the SFC2/OP version show the same errors in game?