That seems bad!  Is it just your SSH information that doesn't get saved?
Like, does your list of includes/excludes and whether you want
encryption and such saved?

Can you provide the file /tmp/deja-dup.settings after running the following:
gsettings list-recursively org.gnome.DejaDup > /tmp/deja-dup.settings

** Changed in: deja-dup
       Status: New => Incomplete

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

Title:
  Preferences aren't saved

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