Well, hmmm. There are only two braze on Ultegra der. FD-6500 a double and FD6503 for triples. And they travel a little different(The triple drops more when shifting down) but I wouldn't think this would cause your problem. You should be able to get the bottom of the cage with in 2mm of the chainring.
I would go to a Trek dealer and look at a 5500 on the floor, maybe you have the wrong braze on mount.
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