Android M weird shared preferences issue

That is because Android M will feature Automatic Backups (old link).

Extract:

The automatic backup feature preserves the data your app creates on a
user device by uploading it to the user’s Google Drive account and
encrypting it. There is no charge to you or the user for data storage
and the saved data does not count towards the user’s personal Drive
quota. During the M Preview period, users can store up to 25MB per
Android app.

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