In testing, I wasn't able to reproduce your problem, though I'm not sure how to use the plugin. These are the steps I took to uninstall the plugin.
1. Installed the plugin
2. Closed Media Center
3. Removed Auto EQ from the windows uninstaller
4. Opened MC and set the equalizer to jazz
5. I played some music, but it never defaulted to "custom" like yours did.
One thing to try would be installing Auto EQ again, closing MC, and uninstalling from windows again. This will sometimes remove elements that the first uninstall missed.