By default I believe Google Drive puts files from third party apps (like Duplicati) into their own area separate from your normal user files - this helps keep your own files secure and inaccessible to the third party app. (This is a good thing in case something goes wrong with an app update or it gets hacked.)
The short answer is that if you want Duplicati files to show up with your other docs, then you should use the “Google Docs” button in the OAUTH process.