I am having trouble reproducing this. Can you please send in your .shipcfg file for this ship?
The .shipcfg file should be located in /My Documents/My Games/GC2DarkAvatar/Ships.
It will begin with SX_UD_ (where X is a number) and have the name of the ship after that.
Please send that file to gc2bugs@stardock.com. Please provide a link back to this forum post in your message.
Also, do you rotate the part before putting it on the ship or after? Or does it make a difference?
Thanks in advance.