This drove me nuts tonight, I could not clear a bounty, even though I paid it in a system with no presence of issuing faction. Then I found my problem, on foot stuff again.
As a law abiding bounty hunter I killed smugglers as ship mission assigned for me to do, but one of the ships, that counted as mission objective, set me a bounty for murder, but mission accomplished. At an interstellar factor, I paid off the bounty on foot at a console in the concourse. I like getting out my ship once in awhile. It reported no bounties. I get to my ship, I find bounty still active on the external panel for transactions, can't land at my "home base". But wait, I try to pay again from my ship by Starport Services, but Interstellar Factor has been updated there, it shows no bounty. But the left panel reports bounty. I visit my home system, I'm still "wanted".
Reading this thread, I took the advice and logged out, logged back in immediately, and the ship external panel "transactions" now has no bounty!!! What the hell! It kept me out of my home system even though this bounty was paid and cleared! The foot part does not coordinate with the ship part very well at all, unless I relog? Come on. But it foot payment updated with my ship Starport Services, so I didn't pay the bounty twice, it just didn't clear it without a logout.
If I never left my ship, I might not have experienced this, I think, but who knows. Serves me right. As VR user, foot is so, well, sub-par to the ED experience. But I can't resist to step out from the cockpit once in awhile...
I so love this game, and sometimes I so hate it. But though it has so many bumps and lumps, it still is beautiful to play. Most times...