I've been seeing in a lot of the comments that people have been having issues with 2.0E, and particular issues with missile trails and other graphics problems. Please lower your graphics settings; putting them on 'Highest' is an issue for some people, SoGE is more system intensive than stock Sins. In addition uncheck "Use Colored Skyboxes", "Use Deep Space Skyboxes", and "Bloom Enabled" from the Effects page; these should be off in order for the mod to display correctly.
If you find one, after tinkering with your graphic settings, I request that you report it in SoGE's testing forum, or on the mantis bug tracker, with whatever information you have; the ship in question, a picture of the issue, anything is appreciated. I want to stamp out these issues, but I cannot do this without your help! The testing forum can be accessed here: Forums.swrebellion.com