Thank you for contacting us and I apologize for the inconvenience this has caused.
As a potential workaround, you can try the following steps:
1. While in Sector Space, setup your desired powerbar/skillbar setup
2. Then move to a new Sector Block (do not transwarp; enter a mission; PvE; STF; etc. Just warp to the next Sector Block.)
3. Open your character window (press "U") and select your current ship
4. On the lower-left corner of the character window, click the button "Switch Starship"
5. Go back to your character window (press "U" to re-open it) then Select your current ship
6. Wait for the "Switch Starship" cooldown to finish, then click it again to switch back to your main ship
7. Go back to your character window and select your current ship again
8. Select the "Loadouts" tab, and then save your current configuration
I also suggest posting this as a bug report in our forums to help our QA team in the investigation of this particular issue. Here's the official Bug Report forums link: http://sto-forum.perfectworld.com/forumdisplay.php?f=69
Perfect World Entertainment