Sorry about the previous response, I neglected to mention the specifics of the registry entry in question.
The entry will need to be under HKCU somewhere. It can be anywhere, but I would recommend something like HKCU\Software\YourCompany\.
Basically, this takes care of the situation where another user logs in and runs the application from an advertised shortcut--since their HKCU hive will be different, the keypath will be missing, and you'll get AutoRepair.