Did your pain begin before or after you changed saddles? Did you adjust your saddle height to compensate for the difference in "thickness" of the two different saddles? You should measure the total distance from the top of the saddle (using a clipboard on top of the saddle) to the center of the botom bracket. Depending on the design of the saddles, you might need to move your seat post up or down with the new saddle.
At this point, I would recommend getting re-fit. And I have to endorse Erik Moen as well -- he's the best in the business in the seattle area.