Atom Package Settings Not Saving

Very new here, trying to configure Atom based on CoreyMS tutorial. None of my package setting changes are sticking:

  1. python-autopep8 - Format on Save - unchecks after Atom restart
  2. Kite - Show welcome notification on startup - rechecks after Atom restart
  3. Linter Flake8 - Executable Path - reverts to default after Atom restart

Any help is appreciated.

Re-applied Full Control in Advanced Security permissions to all child objects within .atom/Packages folder, which appears to have fixed the issue.

I have the same problem. in Kite the field Enable codefinder decoration rechecks after atom restarts.

Can you please give more details on your solution?