At high temperatures the carbon will bond with and remove the oxygen in the metal oxides used as colorants in the glazes. This loss of oxygen results in a change in the color of the glazes because it allows the metals in the glaze to be seen in an unoxidized form.
A reduction atmosphere can also affect the color of the clay body. If iron is present in the clay body, as it is in most Stoneware, then it will be affected by the reduction atmosphere as well.