Join Date: Oct 2004
Location: Camas, WA
Bikes: Black Cat SS, Salsa Spearfish, Trek 520
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Everything should be centered correctly if it was built properly. Since you said it arrived adjusted, I would first try to re-center the wheel. Loosen the quick-release skewer (or axle nuts) and see if you can manually center the wheel.
If your bike has track ends, the wheel may have slipped forward from pedaling, causing it to be off center. Be sure to tighten the skewer or bolts adequately to prevent slippage.
On certain brakes, the distance to the rim can be adjusted using skinny or fat washers. I probably wouldn't pursue this option with your bike since you said it came adjusted properly.
As a last resort, did you break any spokes? That would cause the wheel to become off-center.