Probably an issue with how you have the Detail settings applied to Brushes. Make sure all your hull brushes are set to Detail Level 0. Other internal Brushes are best set to Detail Level 1.
Some exceptions make this confusing, especially Brushes bound to objects. That is, Translucent World Models, Doors, anything else, etc that requires binding to an Object, even if those Brushes are internal, they should be Detail Level 0.
That's the only thing off hand I can think of right now.
-Windebieste.