Hello ShartRate,
Pretty sure I know what your problem is... I have a Trek 4.7 (also a carbon frame) and had the exact same problem a little while after buying the bike (from new). It seems carbon frames are prone to this but I've cured mine now.
Initially I took it back to the bike shop; they tightened the BB bearing cups into the frame (with that Shimano tool - which I now have 2 of), and for a while it was good. Then it started again so I did it myself this time... Nearly broke the veins in my hands getting the cups out, as the shop had overtightened them way above the 50Nm recommended! Anyway, to keep a long story short-ish, I cleaned the threads; tried them dry; tried them greased; tried them with a greased washer (in case the noise was from where the cup face sits against the frame); some worked for a short time until I finally cured it...
Basically, the noise comes from the very slight movement of the bearing cup's threads against the opposing threads of the bottom bracket in the frame, and this noise is amplified (massively) by the thin carbon walls! So I went to town cleaning all the sets of threads - using Isopropyl (which is pure alcohol, that you get from a chemist). I then coated the cup threads with Loctite 641 Bearing Fit! I'd already used this to stop the bearings 'moving' in my Zipp 188 hubs to great effect, so knew it would 'lock' the thread better than even thread lock! (I've since gotten rid of the 188 hub and replaced it with a Tune Mag 170. Way better!)
I did that months ago and have not had a single click or pop since, no matter how steep the hill and how heavily I'm stomping on those pedals! :-)
darth.