My original H2 geometry Madone (52 frame) developed an issue with the isospeed decoupler, which Trek couldn't resolve. Their customer service did me proud however and they upgraded the bike to a H1 frame for no extra cost.
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They never got to the bottom of what was causing the problem. The symptom was that it squeaked loudly. The whole area was dismantled and replaced, the bearings were replaced, they even suggested at one point that it was the bottle cage bolts causing the problem. Nothing solved it however so eventually I got fed up and told them it either needed to be sorted once and for all or they needed to replace it. It went back to Trek's QC centre in the UK, was with them for two weeks, it came back allegedly cured and.... 5 miles down the road it was squeaking again. I videoed it, sent the video to Trek and to be fair to them they then bent over backwards to resolve the situation, hence I ended up with the H1 and a replacement set of the integrated bars (I wanted a narrower set) for no extra cost. Painful, but I'm happy with the final outcome! My LBS had by this point also worked out how to make sure the cables don't rattle which drove me bananas on the first bike, so it is (touch wood) a silent stealthy speed machine.
My Warranty Replacement Madone H1 - Weight Weenies