It sounds like the indexing or the cable tension is not adjusted properly. Check out the instructions at http://www.parktool.com .

For what it's worth, I had a Trek 1000 with the same components and it shifted well. Last year I got a Trek 5000 with Ultegra FD and RD and a Bontrager triple. That bike never shifted well until I replaced the crank with a Shiman R600 compact. Now it shifts great.