So, I've skimmed through the thread and the Trello and I have a bug might stem from the same problems as this bug. In what the logs seem to differ is, that my game breaks while loading the PlayerShipConfiguration and the 'warp' loading animation just freezes. You can find my Log here. This only happens after at least one game with the custom ships.
My game's version is Alpha 0.8.03_UPDATE_3 KIRK. I am running Win10 64Bit. (Do they even do 32bit anymore?)
I sadly don't have repro-steps, as I cannot pinpoint when exactly things start getting messy. With only 1 or 2 custom Configurations, things seem to laod fine, but as soon as I start going to town with the custom Configurations things get messy. Apparently there's also issues in the Hangar, where clicking a saved Config loads the wrong Configuration (in my case, the one to the right) so that might be an indicator of what could be going on?
According to the logs, you guys create new Scriptable Objects with the new parameter, but afaik that does not work for Scriptable Objects, which needs to use the .createInstance method, as the logs suggest. (layman here, still studying, but I have come across SO's before.. )
I will update the post if I can pinpoint what's causing this and if I can repro it.