I'm having the same issue, I set up the loadout, switch to another ship, set up a loadout there, then when I switch back and forth, neither ship has the correct bridge officers and some bridge officer slots are completely empty. I'd say there are some bugs to work out in the loadout system still..
I'm having a similar issue, my romulan's head (skin only) flickers blue and then back to normal, happens frequently while in DX11 mode and has been happening since I started using DX11 a couple weeks ago now. EDIT: oh yeah, this is on LIVE.