Join Date: Jun 2009
Location: Pittsburgh, Pa & a little bit of Cali
Bikes: Kona Dr. Dew '09
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The discs should break-in within about 100 miles or so. If you still find they're not gripping or engaging well, you might have to use the barrel adjuster to fine-tune how soon they engage in relation to how hard you press the levers.
One of the PITAs about disc brakes, is their tight adjustment tolerances. If you remove the wheel and don't keep the skewer tightened exactly the same as it was previously, you're at risk for throwing the calipers out of alignment with the disc. You can experiment with the skewer tightness by adjusting the nut in small increments to get the brake back in alignment; however, sometimes it's easier to make a minor adjustment to the caliper centering. Typically, you just loosen the bolts that fasten the caliper horizontally, squeeze the brake handle, and retighten while still squeezing.
FWIW, my best advice is recenter the brakes, buy a bike rack for your car, and don't take the wheels off.