I am having a few problems with the hayes mhx 2 brakes on my raleigh m80. I just repacked my front hub, and cleaned the rotor and pads with rubbing alcohol. First, when the front brake is applied, it feels like the brake is grabbing and releasing rapidly, causing the front end to shake. It feels like a warped rotor on a car feels like. The rotor is pretty straight, less than 1 mm side to side movement. I can feel this while riding, or while pushing the bike with the brake partially applied. It also does not seem to have the same stopping power it used to.
The second problem started before the repack and cleaning. When I apply the rear brake, it makes a sharp click noise. It appears to happen when the brake pads really grab the rim. once it clicks once, the rotor has to be spun fast for it to click again. repeatedly hitting the brake while the wheel is stationary does not click.
For the chattering pads I would try to run the break-in procedure. Do about 10-20 hard stops from speed and see if it helps. Make sure your front brake is safe first. You don't want it to unexpectedly grab too hard and flip you over!
The rear click noise is probably one of the pads being shifted forward slightly by the disk as it grabs. If so, it's not a big deal.