Are these brakes avids? bb5 or 7? I use the bb7 and the inboard pad is static when you depress the brake lever. So its only the outboard pad that moves when the brake is applied. Therefore to get correct alignment...first before you loosen any caliper bolts loosen the outboard pad dial by 5 or 6 clicks, and then tighten the inboard pad (the one nearest the wheel side) by 5 or six clicks. Now loosen the caliper bolts(so that the whole caliper unit can be wiggled side to side by hand); Now apply the front brake lever, and keep the brake applied whilst you tighten the caliper bolts back up; release the depressed brake lever at this point.

Now unscrew both the inboard AND outboard pad ajuster screws by 4 or five clicks each side. Now it should be ok if they're avids.