Alright, I've manage to reproduce the error.
The issue lies with savegame compatibility which unfortunately my testing didnt catch because of how I tested it. Here's the issue:
If you install and load up from a savegame any
pre-existing ships will have broken docking. All
newly created ships will function 100% properly. My testing consisted of loading up a savegame and then spawning ships in front of me to test, thus missing this issue. I apologize for being an idiot.
The current workaround is to install Cycrow's cheat package (
http://forum.egosoft.com/viewtopic.php?t=216691 ; requires the plugin manager
http://forum.egosoft.com/viewtopic.php?t=218121 ) make yourself a new version of the ships you want fixed, transfer wares over from your old ship, and then destroy the old one. I'll try to work on a script that will run around and destroy/re-create all affected ships in the universe automagically for you. Unfortunately I'm
not a scripter though so that's going to be a long ways off and require a lot of testing...
So, if you're not comfortable with nor interested in running the cheat package I guess savegame compatibility is broken at this point. I'm very sorry for misleading you. :-\
I'll update the first post now with the savegame issues + uninstall instructions if you can't be bothered.