Answer:
To all the folks out there with Onkyo protection mode problems:
Most likely you have shorted speaker wires either at the receiver or at/in the speaker.
Protection mode prevents damage to the amplifier by shutting down output when there is a short circuit in the output wiring. This should reset itself if you power off, unplug, fix the problem in the wiring, plug in and power up.
If you need to use an Ohmmeter to check each speaker pair remembering that the speaker itself has resistance on it. If you get an overload (OL) or fluctuating readings on a VOM there is a problem. Should be less than 10 Ohms from the amp side with the wires removed from the amplifier or an open circuit with all wires removed from both ends.
The protection circuit is very sensitive and will detect even a partial short. A damaged voice coil in a speaker will do this also since it detects resistance. The protection mode may also activate if the unit is turned on with no speakers attached. My information says you shouldn't need to reset this it activates a check each time the amp powers on