Well according to the website, your bike came with an Affinity 1 WSD with steel rails. None of the saddles they sell individually has steel rails. Very interesting. I will ask the next time I'm at the LBS to try to find out how the stock saddles differ from from the other Affinity saddles.

But yeah, I think it still makes sense to play around with the position and tilt a bit, to see if you can improve things. Even if it doesn't resolve the problem completely, you might learn something that helps you figure out what saddle to try next. And in the meantime you might make it less uncomfortable while you're looking for a better one.

I found that moving my Affinity R forward a few millimeters caused soreness on the pubic bone as well as some chafing. It's amazing how small changes can have such a big impact.

BTW, I was going to buy that same bike, but they had a 2010 Madone 4.7 on sale for the same price so I got that instead. It really is very nice!