I just sold a 50 tons of driver ammo to the Ganymedian Anarchy station, then went back to Enc for more ammo.
When I got back to Gany station, they told me I shouldn't have come here.
So I exited to the main menu and loaded back in to reload my save to be back on Enc. Then went out to Gany station again, and then they accepted me and did business. The specific line they said was "Didn't expect to see you back here again" or something along those lines.
TL;DR: seems like saving and reloading changed my reputation with the Ganymedian Anarchy station?
I'm wondering if this isn't because I've had the same save file for so long