On Windows, you can press Alt+F4 to shut down Extension Manager. On Mac, press Command+Q. Then you can delete the preference file and restart Extension Manager. The file location is: C:\Users\<UserName>\AppData\Roaming\Adobe\Extension Manager CS6\Configuration\exman_uiPreferences.xml (on Windows) or /Users/<UserName>/Library/Preferences/Adobe/Extension Manager CS6/exman_uiPreferences.xml (on Mac).
If you are using CS5 or CS5.5, please change "CS6" above to "CS5" or "CS5.5".