there's no "factory reset" per se. you can try putting the remote in safe mode and upgrading firmware. take out the batteries, hold the OFF button and place the batteries back in or plug in the USB cable while holding the OFF button. you should eventually see a message on the LCD that says SAFE MODE REQUESTED. if the OFF button doesn't work, try the OK button.

it could be a remote problem so you might be better off contacting harmony warranty.