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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 Terminal.app _before_ running Sage. To be more precise:

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

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