Looking at this further I see what is going on. I have file monitor pulling things into my music collection from the "new" and "library" folders. The key part there is that it's adding them to my music collection. From there auto-organize is organizing files in said music collect...

No, I've already stated that auto-organize is not configured on the new folder. Hence why I'm calling this a bug.

Using auto-organize. If I have the new folder monitored but only the library folder set to auto-organize then it transfers the files over from new to library folder. Pretty sure this is just a bug with the way I'm using auto-organize to essentially import my music from the new folder. If I turn off ...

I'm not sure what you mean by using auto-organize manually on the new folder. The only place I have the new folder configured is in the file monitor. I'm not using auto-organize on the new folder at all, manually or otherwise.

The "Delete emptied folders" option is deleting folders from a different location than what I have specified in the auto-organize rules directory. I have the folder monitoring set to monitor \\nas\music\new and \\nas\music\library but I only have auto-organize set for \\nas\music\library. ...