Your problem is probably not a memory issue. Can you please send your debug.err from My Documents\My Games\GC2DarkAvatar, a zipped save game with a ship design that exhibits the problem and a screenshot of what you see when you try to design a ship using the template to email@example.com? Please make sure that the save game is zipped or it will get corrupted.
You can create a screenshot in game by hitting CTRL and the Printscreen button. It will be saved to your My Documents\My Games\GC2DarkAvatar\Screenshots.
Cari - I've had this problem as well - but I can't reproduce the bug as it vanished on a reload, the fleet bug and the 'missing part bug' seem to happen together.
I'll try describe the problem - (Playing Drengin DA campaign), when designing a ship all the parts show in the bar across the top of the design screen as you go - except the extras which show only blank boxes - the extras show on your design fine.
The second part of this bug is that the 'yellow engine' extra part vanished after you fitted more than one.
Windows XP (service pack 2)
Intel Pentium HT 4 (dual core) 3.80 GHz 3.79 GHz
Nvidia Geforce 8800 GTS (320mb) driver 163.75 whql
2 GB system ram
Xear 3D onboard sound (latest driver)