I experience a similar behavior. I've setup Deja Dup to backup daily on an 
external drive (no data encryption). The scheduled backup often fails. When I 
check the preferences I can see that the destination folder has been reset to 
Amazon S3. Other preferences are saved (encryption, schedule).
This on 11.04 with Deja Dup 18.1.1

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https://bugs.launchpad.net/bugs/774897

Title:
  Preferences aren't saved

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