I just installed this game and I too am having problems with disappearing and glitching ship parts. However, it seems that in my case all ships are affected, even outside the ship builder. To start with, my colony ships is without visible colony modules:
When going into the ship yard to see what is going on this is what I get:
Drivers are updated, game has been re-installed 3 times and I even switched from the steam version to the stand-alone client. I still can't figure out what exactly is happening here.