Problems after malware attack

After cleaning up my computer I have had problems with a few programs, unfortunately including NZBD. I have got it running again, but I am still having some problems.

Basically I can run it as a service, and not be able to connect to my files, or I can stop the service and NZBD can’t connect to my indexers, to update, or basically anything.

The most relevant error message seems to be: Failed to get response from: http://services.nzbdrone.com/v1/SceneMapping Unable to connect to the remote server

Is there something I can do to run it cleanly without the service?

Sounds like its not cleared up to me. As someone who gas dealt with malware before, its not truly gone until you reformat.

Not being able to access files sounds like: https://github.com/NzbDrone/NzbDrone/wiki/FAQ#why-cant-nzbdrone-see-my-files-on-a-remote-server

As for the issues when not running as a service, I’m not sure, but could be the malware, since the same code runs no matter how you run drone.