I just had the same exact problem on my 07 Lemond Zurich w/ Bontrager Race wheels. On mine, it would only make the clicking noise when I was standing. It did this the first day I got it. I gave it a few hundred miles, lubed nipples, etc, and it wouldn't go away. The mechanics tried everything with that wheel, swapping out all the guts in the hub, checking spoke tension, etc, to no avail. In the end, the wheel was replaced under warranty with no problems, and the new wheel is silent. Bontrager may have had a few hubs slip out with some type of defect, I would ask for a replacement wheel if they can't figure out the problem. I don't know how old the bike is, Bontrager has a 2 year warranty on their parts.
PS The service at Trek Bicycle Store of Estero FL is totally awesome!