This has all the symptoms of what i've been calling the structural directX model flaws at random when i manipulate(d) them in the shipyards, too.
It's not the card, the OS nor is it a bug related to OUR pcs... it's simply how **some** of the ship parts were saved by SD devs and integrated to fit each other's between code principles found in three different expansions.
The best example for this 'weird' graphical effect is the discarded Troop Carrier model from DL days... the side and top sides become invisible cuz the file itself & its UV mapping material & texturing slots (for those polygons) aren't in the correct format. Indirectly, it's as if you'd take a flat rectangular surface, paint the top White and paint the "underneath" black... but when you look or take a photographic picture of both sides, Black becomes completely invisible.
Even i get these artifacts at times (strangely in new games, they may or not show up!), it MIGHT be caused by a slow card or lack of memory, shaders & what else (and if you should ask, it is a NVidia GeForce 8600GS and it is absolutely enough and solid to support GC2 all the way to TA) but i can prove to anyone at SD that a few of their **old** (as in DL or DA) structures are simply flawed or incompatible enough to create these random glitches.
In every other situations you seem to describe, it's absolutely normal to get semi-transparent structures and visually incorrect (depending on your perception, btw) drag&drop split seconds of invisible stuff in a not-bugged shipyard like everyone else.
