I have had this problem for a while now.
I have 2 ships always selected. one i am able to use and the other i am not able to. This is in addition to my shuttle being selected.
I can select and use all but the second selected ship. When i go to beam up to my ship it goes to unusable ship's bridge. This prevents me from using my tuffli or any other ship's bridge. It also will not let me change the look of any of my ships.
Screenshot
"We've Been Looking For The Enemy For Some Time Now. We've Finally Found Him. We're Surrounded. That Simplifies Things"
- Lewis Burwell "chesty" Puller
How Romulans Should Choose What Faction They Are In
Comments
I had a similar issue after LoR launched on one of my Alts.
I was able to get around the issue by changing my "primary" starship to a totally different ship than the two listed. (This gave me one ship and one shuttle) I then changed my primary ship again to the one I wanted to fly, and the issue was resolved.
Hope the same workaround might work for you!
http://www.youtube.com/watch?v=_PVHh5RU-gE
- Lewis Burwell "chesty" Puller
How Romulans Should Choose What Faction They Are In