rear-wheel/hub specialist--metallic scraping sound coming...

If all else fails, the rotor itself could be out of round, and rubbing not on the pads, but on the caliper itself.

Bingo, that's what it was. I went to my LBS where I got the disc brake the other day. The bike mech. was really helpful and looked at my bike. He tweaked it a bit and then said something about the pads rubbing, but I wasn't too satisfied with that answer because the pads weren't rubbing! I know there was clearance on either side of the rotor! The noise was gone for the time being, and I was just happy. However, before I rode back home, I tested the rear wheel again for any weird metallic scraping sound. It was back. And so I went back, feeling a bit bad about having to bother him again. He put the bike on the stand again and after spinning the rear wheel, he found out the problem was that the rotor is not completely round! I asked if this was a manufacturer defect, and he said no...or something to that effect. What? How common is this? He said the problem can be fixed by raising the caliper up just a mm up from the black brake mount using two washers. He can do this for $12. I decided to do this myself. Two questions:

1. I got the disc from them and had it mounted by them about two and a half months ago. Should they fix the problem free of charge?

2. Is riding with a rotor that is not truly round bad for the brake unit? Does it pose a safety issue? If yes, should they replace the rotor free of charge? Or is this a negligible problem?

I went home and fixed the problem myself gratis. Thanks y'all.

If they installed the thing in the first place, they should fix it no charge. Might require you bringing the receipt for the install work to prove your point. Rotors don't just go out of round during the course of normal, or even abusive, riding. Warping, yes...but this is not a result of that. No rotor is perfectly round...there will always be imperfections. The less expensive the rotors, the more variance you will find. I'm not entirely sure how much variance would constitute a manufacturer's defect...it depends on the manufacturer's quality control standards, I suppose.

However, since your particular model uses a post mount style caliper and a couple of shims solves the problem, then I wouldn't be too terribly worried. My disc brakes are Maguras with the international standard-type mount. Shims allow me to adjust my calipers laterally. I have no adjustment vertically. For me, an out of round rotor would result in a phone call to the manufacturer (where they'd probably tell me to take a file to the portion of the rotor that is doing the rubbing).

I'm not sure how much damage it would cause to your caliper if you just let the rotor be. If it's a cable-actuated disc brake, it's pretty unlikely that any damage would result in a problem. However, if you have a dual piston hydraulic brake, I could see the potential for the grinding rotor to compromise the caliper and cause a fluid leak. Since you caught this problem and got it fixed fairly soon, I wouldn't worry.