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Georg S. Weber found a problem with the app which is being tracked as ticket #12161. Hopefully this is your problem since we have a fix for it. :-) The problem should only manifest itself if you have not successfully run (a sufficiently new version of) the Sage notebook before. One way to work around it is to start _before_ running Sage. To be more precise:

  1. Quit and if they are open.
  2. Start (located at /Applications/Utilities/
  3. Start
  4. A new window should open in and ask you for a password for the notebook

At the very least this might be @lharris's problem.