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As soon as you rule something out that's exactly what it will be. On a complex chip like that, one section can up and fail while the rest of it goes merrily on it's way, your vehicle engine doesn't die when you get a flat right? I've never seen or touched one, but see if the 5v for the ports is there before digging into the data line mess, where you'll need a Logic Analyzer or at least a scope to see if there is really anything going on there.