[Captain Kwok]

Try Malfador's ship viewing utility. The mask setting only works with absolute black, so you should be able able to catch any erroneous borders etc.

Perhaps a directly overhead light source might help in the final mini renders. Of course, rendering the minis at a larger size and then re-sizing them in a quality image program might also help. You could also try selecting the greyish areas and using a 'saturate' command to see if you can match up the colour with the remainder of the ship.