From your install manual, the "Burnish" period is only 30-40 stops, so you should be beyond that. If the bike is still within a month or two of purchase, I would suggest taking the bike back to the shop and playing dumb. They sold you the bike, they should fix the brakes that aren't working properly. If they say, "they're supposed to do that", I'd suggest checking with another LBS. The other LBS may even fix them for free (depending on the problem) just to win your business (after you explain what the other shop had said).
If it has been longer than that, you can try a few things to see if it is a minor issue. I don't use Hayes brakes specifically, but here are some good starter ideas that may work to narrow it down:
- Clean the rotor - Easily done with rubbing alcohol.
- I use small, single-use, swabs that can usually be found around the diabetic testing equipment at your local pharmacy. Easy to use and easy to carry with you.
- Clean both sides of the rotor. Inside and out.
- I keep cleaning until the swabs come back almost entirely white.
- Check the pads for debris - Pull the pads out and look for rocks, plastic, sticks, or anything else that might have gotten embedded in the pads.
- Clean the pads - Hit the pads with some sand paper to take off the top layer.
- Center the disk in the caliper - This one is in your install/service manual. So for Hayes Stroker Trail brakes:
- Loosen the caliper mounting bolts.
- "Squeeze and hold the brake lever. While holding the brake lever, shake the caliper to position it in its natural centered position over the disc. While squeezing the lever, tighten the mounting bolts." -- Page 2 of the install manual.
- This may be different for your braking system (year, features, etc), so check your manual to be sure.
- Ensure the disc is mounted properly - Check to ensure that the disc is mounted to the wheels correctly.
- From the install manual for Hayes Stroker Trail brakes, the disc bolts should be tightened to 50 in-lbs of torque.
- WARNING: It is very important to ensure the correct torque is used on the disc mounting bolts. 50 in-lbs of torque isn't very much, so save yourself some heart-ache and use a torque wrench. Remember, brakes are important.
Anything beyond that, and I'd take it down to the LBS, let a trained eye take a look (and listen) to them and see what they say.