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I have my caps lock key set to be control on my internal MBP and external keyboard. This has worked well for years. Recently, every time I reboot (and possibly at other times too, haven't paid close attention to the pattern), they get set back to caps lock.

I'm on 10.6.8

custom modifier key settings

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It seems to be caused by a corrupted preferences file. Try renaming ~/Library/Preferences/.GlobalPreferences.plist and rebooting (note that you will need to rebuild some other preferences as well, such as appearance).

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