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On my Lion installation changes in the OSX Control Panel some settings are no longer saved eg. General oder Language. After reentering the Control panel again, the old settings are still in place. Some settings (e.g. Keyboard oder Sharing) are stored correctly.

The problem appeared after installing a SSD as a new startup drive. The user profile in question is still residing on the HDD (/Volumes/Data). In the User Extends settings the User folder is set to /Volumes/Data/Users/username. On the SSD at /Volumes/SSD/Users the is a hard link pointing to /Volumes/Data/Users/username.

Where are the settings stored? I suspect them to be found in ~/Library/Preferences? Is this correct?

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By Control Panel do you mean System Preferences? – Nathan Greenstein Feb 5 '12 at 21:55
Yes, exactly. Sorry for the inaccuracy. I'm using the german language version and former windows user.... – Roland Judas Feb 6 '12 at 8:20

I found the solution:

There were some ACLs gone wil. After resetting ACLs using

chmod -RN ~/Library/Preferences

Preferences are stored are desired.

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I'd recommend running Disk Utility and having it do a Permission Repair on your new drive. This should resolve any residual ACL problems you might otherwise see. – Christian L Feb 6 '12 at 18:19
Christian, thanks for the hint, I used the permission repair previously and it seems this doesn't repair ACL issues below ~/ . – Roland Judas Feb 10 '12 at 14:35

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