This sounds very similar to my issue I discovered last night on my new JTV-89F. When using any of the models, I hear not a scraping noise, but what sounds like a warbling flubby pitchy tone in at a frequency different than whatever tuning I am using. I'll test it more when I get home, but last night this appeared to be happening only on the A string and only when palm muting. When I'm in one of the drop tunings, it sounds as if I'm hearing the standard A pitch, along with whatever tuning I am in. It might not be the actual, A, but that was my first thought when I heard it. So annoying...