I can confirm this bug on a fresh 14.04 installation. Every other day,
the focus-follows mouse and autoraise setting is reset to default. I
have been using this feature on linux since 13 years. It's really
disruptive that settings are just lost.
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PS: I actually seem to have lost the setting mid-session without even
logging out.
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https://bugs.launchpad.net/bugs/1112061
Title:
unity forgets focus-f