My toon on Tribble that has an Odyssey has a curious bug. Whenever I saucer sep, or escort sep my main ship weapon effects disappear. I'm reasonably certain that they are still working, but I can't SEE them firing.
When I rejoin the ship they go back to normal.
So far this has happened in both Starbase Defense and Blockade.
EDIT: This didn't happen when I separated out of combat, but still occurs when I separate IN combat