Comment 8 for bug 194241

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Tom Davidson (tjd-mit) wrote : Re: preferences.xml not a valid XML file, or you dont have read permissions on it. inkscape will run with default settings, new settings will not be saved

I'm not really familiar with Inkscape on Windows, but un-/re-install should work. While you're at it, you may want to upgrade to 0.45.1 (the 0.46-preview releases have some big problems on Windows right now).