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Ensign
Join Date: Aug 2012
Posts: 12
I had the same thing occur. I initially noticed it right after selecting a default shuttle. It added the universal ensign boff from my shuttle to my primary ship options.

Switching between ships after this keeps both sets of boffs active.

I've also noticed that there seems to be some issues as to which ship it thinks you are currently in after you've traveled between bridges. Even from my VA cruiser, it dumps me in the shuttle bridge scene when I "visit bridge". From playing around with characters and ship selection, it really seems to be some sort of crossover issue with having two "active" ships (primary + shuttle).