Depending on what kinds of tweaks you have installed, most of its data will be carried over to your iTunes backup as they're integrated with your system settings and/or application data, both of which are transferred over during a backup of the device. Once you've restored to a stock iOS, you no longer have the tweaks on your device, meaning the settings and such will constantly try to find the correct directory or just execute the code constantly despite the lack of the inlet/outlet that you have when the device was jailbroken.