MandMs05

I realize this thread is quite old, but it gave me an idea of what to look for and helped me fix it regardless. I think it's not to do with any one mod in particular, I think it's any mod trying to overlay a texture in an outdated/unsupported way and Unity has no clue what it's doing so it places a pink square over your spaceship rather than the specific texture or effect it was meant to place. Try removing any mods that might be outdated or that focus on texture placing. For me it was Planet shine (With AVP and EVE), which I believe has some added textures and shaders. Either way, the fact that there's seemingly no one specific mod that causes it is kinda suspicious, so just look for if it adds certain shaders or textures on things (on your spacecraft), or if it has to do with certain mod parts that might have conflicting or invalid textures. Cheers!