I haven't found a way to fix that yet, but since we're running my mod on a closed server and I have the chance to warn the players before hand, here's what I did;
In shiparch.ini all of the pilotable ships have the following mission_property line:
mission_property = can_use_berths
By default the larger ships have can_use_large_moors or something liek that. Anyway, this change lets them use the regular docks. BUT, they don't fit in anything but the planetary docking rings so the players need to be warned that if they try to dock at anything other than a planet with one of the big ships they'll never finish docking. On the flipside, it encourages some teamwork if you have a train full of Niobium and you want to sell it at "The Ring" in new berlin you need a friend in a smaller ship who can ferry the stuff down for you. Then again, with the hold size these things have you can make a nice profit running water and oxygen between planets