I'm getting the same issue with the environmental suit when used in combination with the Romulan Federation 1 top and Romulan Federation undershirt. I don't think my romulan appreciates going topless, or lossing her head over something as simple as a basic EVA... ;)
So, it still appears to use the shuttle name in all NPC dialog, in addition to the character select screen. But tool tips and ship name in the UI use the last ship "made ready".
It is not alphabetical, nor is it numeric by registry. My startship is the U.S.S. Causality NCC-97434, my shuttle is the U.S.S. Holmes NCC-98719, and, as you can guess, I also have the same issue. Edit: in game, it appears to use the last ship that you "made ready". However, the wrong ship still appears on the character…
That is incorrect. My Starship is the U.S.S. Causality, my shuttle is the U.S.S. Holmes, and everyone thinks I'm in my shuttle. It *could* be going by registry number though.... *Edit: Just verified; not registry either.
I'd like to quickly point out that the nebulae issue is still persisting... Windows 7 Ultimate SP1 x64 Intel Core 2 Quad Q9650 (3GHz) 8GB RAM nVidia GeForce GTX 570