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Weird. I would disconnect the negative terminal on the battery and start looking for loose connections. Start at the ECM and don't forget to check the wires under the engine for damage. When you're done, reconnect the battery and clear the DTC's with your tool. You could have your tuner do a WRITE ENTIRE to your ECM and see if that helps.
Post your complaint on the HP Tuners forum and see what the pro tuners say.
Good Luck
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