I tried that. It helped little but I have now (after delete and reclaim the Odyssey cruser) on the bridge only the officers I have assigned for tactical stations (5 for Odyssey). The rest are random NPCs. I used to have the bridge full of Boffs from my list even if they "do nothing"...
Same issue. Department heads are changed each time I change avatar/ship view. No problems with changing instances, I have to change type of view (ship to avatar or avatar to ship) to start this bug.