How low are you on the front end? Perhaps for the longer events you should consider sacrificing a little aerodynamics for comfort by raising your handlebars and armrests?
I ride anything up to 25 miles in the same position, but raise the bars about an inch for anything longer. It doesn't help the saddle area so much as my back and neck.
If you are riding the same setup, are we to assume that the pain kicks in after 15-20 miles? One solution might just be to ride in that position more and you'll get used to it. Generally with a position as extreme as a TT, you know if the saddle position isn't right within a couple of miles - ideally you do not want this to change much between bikes.
Maybe a picture will help?