Anyone else have this problem? When I make a ship, sometimes it looks one way while it is being edited, and then snaps to a different look when you save it. Open it up again in the designer, 'use' the design, etc., and you see the original ship you wanted. Save it again, and it looks wrong everywhere.
This seems to be related to using custom parts: a similar problem happens in the designer, and I'm sure someone by now has realized the custom parts break sometimes when you adjust the scale.
The original ship: the gun turrets are custom parts (really lame ones):
This is how the ship looks in the designer once you save it:
Here's how it looks in the shipyard:
And here it is in space: