I have artist/album as the download selection, but when autopar runs it moves everything downloaded back to the base folder
Any files that gets repaired uses the "UnRAR" path so, if I had to guess I'd guess when the files are repaired it then sends them to the default unrar path. I'll give some a try and see what I see.
I think there's a bug enabling and disabling servers. Clicking on the "green lock" and turning into the "red circle" doesn't actually disable the server and the reverse doesn't enable the server (it indicates that's it's disabled, but it still download files in the download list using it). Only right clicking the server selecting disable/enable from the menu actually does it.
I believe you're right. You probably need to use the server options for now.