When light hits photosynthetic organisms photosynthesis occurs, which absorbs CO2 and O2 is given off which tends to increase pH. With lights off respiration occurs from photosythetic organisms which causes CO2 to be released. The CO2 release causes pH to decrease. So by using 12 on 12 off you can (sort of) limit the pH swings in your tank. I believe this is the theory behind it, but I could be wrong. I'm sure someone will straighten me out if this is completely wrong.
-Walter