Yamaha PEQ
Nick,
I have a lower end yamaha (HTR-5860) and it has an option for a manual fixed band EQ in place of the automatic PEQ. On mine, there is also a way to turn the PEQ On and Off in the setup menu. Many people are not too impressed with the capabilities of the auto EQ, so I wouldn't worry about this feature too much.
Check the manual online for the factory reset procedure. Ususllay you have to hold down a couple buttons when you power on the receiver.