I rode the '08 Madone 5.5 (Performance Fit) which is outfitted with Dura-Ace, a few weeks back when I was looking to buy a new bike... Ive had 3 treks since Ive been road riding (pilot, 2 madones) and its finally hit me why many people dislike trek... They are way too commercialized, and really have down right dull designs... and definitely too many bland proprietary components... but when you get into road cycling they sure do seem like the best choice...
But to answer your question, it does seem to have improved stiffness over the last generation Madone. Lighter as well. However I ended up just going for the '07 Cannondale System Six Team Si 2, as I wanted a change... twas a little more expensive but a WHOLE LOT stiffer... and weighs nearly a half-pound less than the '08 madone 5.5... and the C'Dale comes with the notorious Mavic Ksyrium ES wheels... bling bling!