Maybe it's the derailleur. Maybe your old FD accomodated the 40T middle ring, and the new one doesn't. I think I'm having a similar experience; I had to replace a 105 triple FD from '03 with a new Ultegra triple when I got my frame replaced; fatter seat tube. '03-vintage bike came with a 52-40-30. When I built up on the new frame, and set the height of the der according to the little guide sticker, the inner plate hits the teeth of the 40T chainring. I didn't know until reading this thread that 39 is the new "standard" for the middle. For now, I've just raised the derailleur up on the tube about 2mm; it's outside the "range" according to the guide sticker, but it shifts alright. Is that what the shop did to make yours work?