HTFU is the saying, but don't ignore knee pain - obviously something isn't right! Did you up your mileage when you got the new bike or anything like that?
What's different about the fit anyway? I measured the distance from the crank to the bottom of the seat post bracket, the distance front he tip of the saddle to the bars etc. when I moved to a new frame and tried to get it as close as I could when I changed bikes. Had some front knee pain and raised my saddle 5mm, which seems to have helped.
You probably need to find a place that will do a real fitting for you, and not just a bike shop employee that says "OK, stand over that one, yep, looks good" (I have no idea what they have already done for you nor how involved it was, just guessing)
Here's some light reading for you in the meanwhile. Nice bike btw.
http://www.cptips.com/knee.htm