Update:

I talked to the shop foreman at the Honda dealership that I usually go to - Arrowhead Honda. I had gotten the rear brakes replaced and the rotors re-surfaced there in December. We chatted about my problem, and I was looking for some advice from him. Since his shop did the work before, and I was having the problem now, he insisted that I bring the car in, because he wanted to see what was causing my problem, and see if it was something that they had never seen before and if they could learn something. He was concerned because they are new pads (only 7 months old) had they had machined the rotors for me.

So I stopped in today, and a tech drove around with me in the card and heard the grinding that occurs on my right rear as I break (that's why I wanted to machine the rotor myself). He said there was definitely something not right. So we drove back and they put the car in a bay.

My service rep - Anton, came back an hour and a half later and said that they figured out the problem - they had never seen it this bad before. I guess that the Honda OEM pads today cannot contain Asbestos (did I spell that right) because of the EPA. Because of that, the semi-metallic formula that they use isn't as friendly, and what can happen is that as the brake dust leaves the rotor it can become static-charged, and get sucked back onto the rotor. The dust then clumps on the rotor, and it my case it got so bad that it was cutting into my rotor. So they cleaned the thing off, and moly-coated the brakes again in the rear, and no grinding!

My rep insisted that I call him on Monday and update him on how things were, and that even if I don't have the problem anymore he really wants to machine the rotors again for me just to make sure things are OK.

Still planning on replacing my front pads next weekend once the pads arrive in the mail - HondaPartsForCheap.com - a dealership in Missouri. Good discounts off of normal retail on OEM parts.