so there is an issue where your action bar (above your Boff bar) is not saving under "normal" circumstances. There IS a temporary workaround for saving your current skills.
To help resolve this, kindly follow the steps I've written below:
1. While in Sector Space, setup your desired powerbar/skillbar setup
2. **Optional due to testing**Then move to a new Sector Block This part however IS important (do not transwarp; enter a mission; PvE; STF; etc)
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 *Optional (?) as I have not saved loudouts post configuration and it still saved skill slots*
Thanks to GM Urizor
*copy-pasted parts of original email, edited due to testing (Optional stuff)