OK, there's a weird thing going on with subobject rendering and alpha textures. Now, under 3.6.5 and the LOD rendering distances, unless you got to point-blank, you would never see anything of Bob's Deimos but its LOD1 mutli-part turrets. On the other hand, Bob's Hercules displayed apparently normally under 3.6.5, because you were always seeing LOD1. If you zoom in so that LOD0 is visible, suddenly the ship disappears and all you see is the cockpit sub-object. Now, since you've reverted to the previous LOD viewing distances, the LOD0 of the Deimos is now typically visible, but the LOD0 of Bob's Hercules only displays the cockpit sub-object. Also, the alpha textures on the Deimos are completely invisible and you can see right though the ship there. I don't suppose that these will be easy to fix eh?