a lot could be causing issues with just the file(s) vs ini files (particularly the loadouts.ini and shiparch.ini)… are all the original hardpoints still entact by their default names? I know trying to mount a gun or even shield in the loadouts where the hardpoint is not defined in the cmp, 3db or even shiparch.ini can cause funky things to happen. Also check all the references match the file names within the files by using Freelancer XML Project…
Given the fact that replacing your clone w/ the vanilla model and no longer have issues kinda rules out the lack of definition in the shiparch.ini, but not a missing or miss labelled hardpoint in the 3d file. Also could be trying to reference something that hasn’t been properly linked to the new 3d file (as I mentioned at the end of my first paragraph and using Freelancer XML project to make sure everything is linked correctly). The fact the vanilla model does not crash also suggests that it most likely is not an issue with the platform it’s running on, but the 3d file itself. Lastly, I’ve heard of issues similar if and when a 3d file isn’t made with triangular polys, so that’s something also worth checking… tho I do believe I recall milkshape only working with models that use triangular polys…