I've had nothing but shifting problems with my Ultegra STI shifters on our cannondale. I put in a new front derailler cable and that helped a lot. I used the thickest stainless one I cold find (on bikeman). The longer cable is an issue, I'm convinced. This winter, I'm tossing the crappy Shimano shifters and Going either with bar ends or with Campy brifters and a travel agent.
I put osme of the blame on the Truvative cranks as well, which don't have perfect chainring spacing and wobble a bit.
People may tell you that the shifter cable don't stretch (I'm not talkng about initial break in stretch, I'm talking about lengthening with increased tension), but they do a little, and with such a long cable run, it will effect things. For me, it's rubbing in the gears you talk about.
Sheldon