Not sure the why or the how. My warlock's ship shader looks fine when I am in my inventory but the completely wrong shader is applied sometimes while I'm in orbit. Low priority sure but figured I'd say something.
Leonid MV
Golden trace shader
not sure what's applied in orbit, something dark green/light green vs golden trace's grey/gold
EDIT: is it the lighting by Nessus and "working as intended"?
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Ive had had this same problem, and worse. I finally decided to use the last of my favorite shader (tarnished copper) on my exotic ship because i figured i would probably keep it around for awhile. But just after i went to crucible and was waiting on the loading screen, the ship had no shader. It just completely removed it altogether. This needs fixed now, because ive wasted 3 or 4 more shaders on it now.