Presumably you installed a new cable and housing, too. Perhaps a housing ferrule wasn't set all the way onto the housing. The first shifts compressed it into place, and now it's acting like the cable is too long. Try resetting the cable again. First tug on it pretty hard a couple of times to set all the ferrules into place, and the ferrules into the stops. This is a good time to practice limiting the torque on the pinch bolt--repeated tightening of the bolt will fray the cable.