On the host app's second launch, Sparkle asks the user whether to automatically check for updates, then sets the value for the preference key SUEnableAutomaticChecksKey to the user's answer.
But Sparkle only uses its own SUUserDefaults object to set the preference; thus, any UI controls that are bound to the preference through NSUserDefaultsController don't hear about the change.
The fix is to set the preference through NSUDC. I'm attaching a patch to trunk@r150 to do this.
I've left in the existing SUUserDefaults-based statement in case you need that for something. However, I don't know whether you do; you may want to remove it before committing the patch.