i had an issue where when i dropped the anti- aliasing all the colours got weird and started to blur like retina burn (you know when u move a light real fast and u have an after image?) except on the game it happened for ages
so yeah, go to the graphics tab and play with the settings there.... actually, just thoguht of something.... have you tried to put the graphics quality UP?
maybe its cause the graphics are too low so the ships look funny, i know sometimes i put the quality on low to get really buggy entrenchment to work, and the ships lost all colour (turned grey) and lost most of their definition so...
give it a try good luck