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Well a clean install won’t do much, the installer just replaced the binaries it does not touch your settings.
To delete the Ctrlr state go to your home folder and find the Ctrlr directory, rename it something like Ctrlr_org and start Ctrlr again.
On Windows XP the home directory would be at (assuming C: is your system drive), c:\Documents And Settings\%USERNAME%\ where %USERNAME% is your login to Windows.