one more thought here... I went thru the same thing with my first bike... came to find out it was too big for me... so the top tube was too long... meaning I was really extended to reach the handlebars... and leaning reeeeally far forward, causing the same problems! I actually couldn't pee the first 1/2 hour off the bike... and then it hurt.

Have your fit checked... something as simple as a shorter stem, or moving the seat forward may help... just remember that any moves mean a change in postition all over, so have an experienced fitter do this if it comes to it OK? Good luck with it!