After having had "Boldly They Rode" completely ruined for me (partially my fault), I had to post to vent/ask for solutions on this issue.
First, after doing small craft missions and changing back to my starship, I noticed the game/UI still thinks I'm in my small craft and when hovering over equipment the tooltip gives stats for small craft rather than my starships. The only way I've found to fix the issue, is to dismiss the small craft -- going back to a starbase and changing craft via typical means just doesn't seem to work. Is there a workaround for this?
Second, and this is by far the more irritating one (yet one with the most obvious, albeit time-consuming, fix), is that when changing ships everything but captain powers is reassigned a location on my hotbars. Considering having to juggle captain powers, a dozen boff powers, subsystem targeting, and hangar/fighter controls, that's incredibly annoying and takes 5-10 minutes of my time to fix. Especially for the fact I have to pull 6-8 weapons (that are all on autofire anyhow), and crap that doesn't even need a hotkey (like my trade vessel summon), off the hotbars to free up room for boff powers and such. Is there any way whatsoever to not have to waste time doing this after changing vessels?