/Settings/Preferances/Miscellaneous/Check for program updates automatically
Where is saves a configuration? userdata.omd ? Is it secret? 
prefs.oxc ??
I could wish save my embedded settings in a files.
The "Backup Configuration" is clean saves all? I could wish strongly save good content...
Yes, that checkbox is always coming back after each update. At the moment you can´t do much except to manually uncheck it after updating a version.
Or just turn on the silent update check option and forget about it.