If you successfully close cgminer properly it *should* return to the default values on shutdown. That said, the windows version has this knack of not closing properly. How/why, remains a mystery. Nonetheless the settings will go back to default on a reboot. None of the settings cgminer uses tell the card to keep settings across a reboot.
Thanks. Upon selling and removing my second graphics card I'll reinstall the drivers and will see whether this changes anything and then report back to you.