Are your handlebars the proper height and what kind of seatpost do you have?
The reason I ask is because I was having saddle and shoulder problems and finally had a Serotta fitting done. There were 2 issues with my bike. The handlebars were 4 cm too low and I had a seatpost with a setback so my saddle was too far back. I have a short femur and the setback was putting me in a position to far away from the pedals. So we raised my handlebars and put a zero degree seatpost on my bike. Correcting those 2 things took away my issues. Now the saddle is flat and there is no discomfort. I rode about 4,000 miles after the change and was very comfortable.
I just put a new WTB saddle on my bike and there is no discomfort at all, even with it being new.
Kathi