In my case it was creaking for a while when under medium to high load (if you can call 250 Watts a lot ), then the creaking went away after a while and one day the crank started to feel weird. First I blamed my cleats being a loose fit in the pedals. But one day I decided to pull and push on the crank arm and low and behold the whole crank assembly was moving slightly sideways.
So I took the damn thing apart, thinking that maybe my bearings had gotten loose and while I was trying to unscrew the bottom bracket all of a sudden the whole bottom bracket shell moved with it and I couldn't even get the bottom bracket loose from the bottom bracket shell.

So I completely disassembled the frame and took frame and fork to the Trek dealer for a warranty claim. Couple of weeks later I had the new frame.

Thomas