Nick, sounds like a coincedence to me. I suppose the scraping of the pin on graphite could cause some signal to be sent through the graphite, but even when the throttle is wide open, that frequency would be far to low to cause interferrance. I've had a pin scrape before like this and never had any glitching, only the scraping sound.
My advice is to ditch the JR and get a KO or Futaba radio. You might also try a Novak XXtra receiver and see if that helps. You are still using the JR syntesized radio, right? I sent in an XXtra for replacement, so I can let you borrow it if you want to try and see if that helps.