I'm not sure about how to resolve the conf. file problem. BUT... Don't bother trying to "Restart" cgminer from a running instance. It is a LONNNNNnnngggggGG know fact that, that particular function "ReStart" is/has been broken. If you NEED to ReStart, your only choice is too "Quit" and run .exe again.
not sure if youre talking about windows, but the only time ive ever had this problem in linux is when the hardware has malfunctioned.