This one has me a little stumped…
The episode has been downloaded correctly, is visible in the filesytem and in plex as well and 100% ok and viewable.
What task regulates this so I can test running it manually?
Whats shown in Activity -> Queue? All that information comes from the download client (Queue & History) and should be removed when all files in the download are imported. In the event there are multiple files and one is not imported it should be visible in Activity Queue.
I had forgotten to hit post well before you responded:
They’re getting stuck in the activity queue. If I delete them manually then everything is fine.
So is the issue with Sonarr or is NZBGet doing something funny?
Whats the error/warning in Activity Queue - hover over the icon on the left.
It was the intermediate folder error.
I changed Factory to a random new folder and everything snapped into place 
Thanks for the nudge in the right direction, I had no idea I could mouse over that.