I have tested this on both an iPad 4 and iPhone 5. Basically after you jailbreak, install any JB program via Cydia that has a line item in settings. For example, we will use F.lux. F.lux has an app icon as well as an entry in settings. If you install F.lux, both the settings entry and the app will show. After a full reboot, the settings entry is gone, but the app remains still works. This goes for any JB app. If it has a settings section, it will disappear after a reboot, and even uninstalling and reinstalling the app won't restore the ability to change a JB app's settings. Can someone please verify this and help??