There is an underlying problem with boarding your ship, since the update 12.
I'm starting to suspect it might have something to do with parameters they set with the Alpha 1 build, where code was inserted to prevent players from flying off in a ship. Perhaps it got baked into the update 12 by accident. Don't quote me on that, I'm not certain what it is but whatever it is, it causes a Black Adder error code, "unrecoverable error on transaction server", whenever you try to board your ship. Is this what is happening to you, or is it just that you have cargo that your other ships don't have the capacity to hold?
At the moment, yes, you have to quit to load Horizons, deploy in your ship as per the prompt on loading, then quit to load Odyssey, then off you go in your ship. <phew> But this has to be done every single time you want to dock anywhere. LOL I'm getting landing anxiety >.< Hope they fix this soon I would say it's the most urgent bug currently in the game. That along with ship transfer not working either! (ROFL!)
This is what leads me to suspect that they've templated another game version but forgot the left over code and now it's baked in update12. I could be wrong, but it should be something tiny and simple like that, hiding like a mischievous sprite, giggling at us all.