How can I keep Mathematica 6.0 preferences separate from my Mathematica 5.2 preferences?

Mathematica 5.2 and Mathematica 6.0 share the same preferences by default. For instance, look at the list of recently opened files. You should see that a file created and saved in one version will also appear in the list of recently opened files of the other version.

If you prefer to keep these preferences version-specific instead of shared, open the Options Inspector, set “Show option values” to Global Preferences, and set the "VersionedPreferences" option to True.

Options Inspector Window

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