When you uninstall the software, it removes its files from your computer. It also removes the registry entries in the HKLM registry. It does leave behind the per-user HKCU registry (where the settings are stored). There are many reasons for this. For one, they are impossible to remove. There are potentially multiple users in the system but the uninstaller only has access to the current user. Second, it is important for preserving your settings during upgrade (an upgrade is basically uninstall+install). And finally, it is harmless. No other software reads those settings that are left behind, so they can't affect the behavior of the computer in any way.
So if your active corners are misbehaving after uninstalling Classic Shell, then there is some other software (maybe Windows itself) that is causing it.
If you want to reset your settings, either delete the HKCU\Software\IvoSoft registry key or use the Classic Shell settings dialog to reset all settings.
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