When you start the application configuration manager it loads the dialog with previous configurations.
As a test:
In windows explorer address bar type %appdata%
This will show you the appdata folder for your user account.
In the 'esri' folder rename the 'arcgis explorer' folder to somethng different, and try starting the application configuration manager again.
If this allows it to start, then look at the 'configuration manager' folder in the ArcGIS Explorer folder, one of the files in there, may be causing a conflict.
Mark