I was told by a car audio guy that these cars need reset after batt disconect, he said to disconect batt and touch the pos and net wires together, this will cause a small spark and is normal, then reconnect batt. I don't know if this will help but he is a pro installer and it couldn't hurt to try.

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intek
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2006 E53 X5 3.0i
2004 Volvo XC90 T6
2000 Jeep Grand Cherokee