I have a brand new bike with Hayes CX Expert disc brakes. When I picked it up at the shop, they had dialed the front brake in nicely so it grabbed pretty quick (i.e. without having to pull it right to the handlebar).
I took the front wheel off to put the bike in my car to bring it home. I was very careful not to hit the disc rotor off anything or lay anything on it as I know they can get bent out of true.
When I got home I put the front wheel back on and re-tightened the quick release, but it now rubs slightly at one point when I spin the wheel.
I found I could fiddle with the barrel adjuster and inside pad adjuster to back them off a bit and stop the rubbing but now I have to pull the lever much further to engage the brakes firmly.
Also, when it does rub, it's only at one point in the rotation which makes me think the rotor is slightly out of true.
Finally, when I engage the brake and look straight down at the caliper, I can see the rotor flex ever so slightly sideways, almost like the pads are coming together at a slight angle relative to the plane of the rotor.
None of this seems to be an issue with the rear, and I have had the rear wheel off a couple of times as well.