I would encourage both to submit a ticket as per pshaws request:;
submit a ticket (https://esupport.stardock.com/index.php?/Tickets/Submit) with the save game and the custom faction (and any custom ship designs if any) attached so we can take a look? Thank you.
That way they have more data about the problem on their side and the benefit for you is that they will be reminded to push the update slightly faster 
