Hey Psiyon,
Just went into my save file to do some experimenting. I found the Dockyard info in the file, and surprisingly free transfer was set to true.
<freeTransfer>true</freeTransfer>
This was the only one in the file, and it was contained inside the dockyard loop. I confirmed that it was in the right place by comparing it with a save file from the previous version, and they were the same. I then proceeded to load the previous version and sure enough, I could transfer items from the station to my inventory freely.
I transferred back over to the new version, and then proceeded to set the faction id of the Dockyard to neutral by deleting this line...
<owner reference="../../CampaignOrbitalStation[4]/owner"></owner>
... and replacing it with these lines.
<owner>
<id>neutral</id>
</owner>
Surprisingly, this made it so I could transfer items freely between the dockyard and my inventory. From these results, it seems like either something in the new update is messing it up or the code didn't set my fleet as being a Ceni Six fleet, but I haven't figured out which yet. There is a lot of code to wade through XD.
Now to hack in a Cordelphia