I was having all sorts of noise/stutter issues until I did the following.
1. Make sure your rotors are true.
2. Remove the pads from the caliper.
3. Push the pistons back out as far as you can. Make sure they are completely flat against the body of the caliper.
4. Feather your brakes a little to make sure that both pistons are engaging. If you have a lazy piston continue to through steps 5-8. If both piston engage evenly skip to step 9.
5. Continue feathering until both your pistons are exposed about 2mm. Clean the edge of each piston with rubbing alcohol. Then lube the edge of each piston with DOT 4 oil.
6. Push each piston back in to the caliper and feather them out again. Do this 2-3 times until each piston moves freely.
7. Wipe down the excess oil/fluid.
8. Reset the pistons.
9. Install the pads back into the caliper.
10. Mount the caliper back on to the bike. Try to center the rotor between the caliper the best you possibly can.
12. Insert some shims or business cards between the rotor and caliper.
13. [B]Gently/slowly (THIS IS IMPORTANT, compressing the lever too fast will only move 1 piston!!!!) compress the brake lever. You want to make sure both pistons are moving at the same rate.
14. Once your lever tightens up and your pads set. Continue to compress your brake lever 5-10 more times.
15. Remove the shims and business cards and take a look at your pad/rotor alignment. Re-adjust your caliper via the mounting bolts if required to center the rotor between your pads.
REPEAT STEP 13-14 AGAIN!
16. Now take a look at your pad/rotor alignment. Spin your wheel if you hear rubbing that is a good sign. Re-adjust your caliper via the mounting bolts once more(will probably be required) to center the rotor between your pads.
17. Pump your brakes, spin your wheel there should no longer be rubbing.
If this doesn't work for you the only other advise I have would be to make sure the caliper in on straight. Sand down the fork mounting post and brake mounts a little to make sure everything is level, or else the rotor will not sit completely straight in the caliper.
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