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I'd have to say that, yes, the Power Commander could be the issue. My thinking is at that RPM it wants to transition from one set of fuel mapping to another and holding it there it's going back and forth between the different settings. At least I see it as possible. What the rattle is, could be anything. Even an exhaust baffle. I'd take it to the dealer that sold it and let them hear it. Trying to diagnose something like this over the internet is near impossible. Or at the very least time consuming and frustrating. Live ears is much better. They don't have to work on it just use their ears.