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I added plugins to the panels,enabled composite, and changed some themes, but then when I shut down, none of the settings were saved, and I was back to the default installation.
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you have to enable save sessions and prompt on logout
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Are you logging in as root and then using su to change user?
If so try adding a dash to su, ie:
su - youruser
This will reset all the environment variables and for some reason X likes to use funky nonstandard ones to get the location of your profile directory.
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