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?
Unfortunately, there is no way to fix this yet. Cryptic's idea to "make things easier" does not actually include rational thought about trying to make things actually work, let alone work well.
The entire thing is a problem due to the way that the Cryptic engine handles your ship. The engine treats your active ship as a character, just like your captain or a Boff. Each of your ships, thankfully, has its own data file about what weapons / consoles / etc are equipped, but it has NO data file for where your individual ship powers and Boff powers were located in the power bar(s).
The result: Power bar blender action.
This is another of those things that Cryptic has simply poked with a stick instead of sitting a bug-fix team down to actually work on it.
I have said it before, as have others: The vast majority of players don't care if we get only minor updates (or none at all) if the Devs actually FOCUS on bug-fixes and making the game less glitchy / crash-prone / etc.
Post Script: Please realize that I am not blaming Cryptic completely in this. PWE should shoulder a lion's share of the blame since they are the "great and powerful OZ" around these parts.
I had an idea how to work around this issue but have yet to try it. It seems to me that the ui is showing your shuttle instead of the ship you had when bought your shuttle, as I cannot reproduce the bug on earlier ships I had before I bought me shuttle,
SO I'd guess the easiest way to work around the issue would be to dismiss your shuttle, change ships to one you never use (like your starter ship) and repurchase your shuttle then change back to your normal ship.