I had the exact same problem in my E46 for years. Never could source the problem. I took the amp/sub out and used it in my E31 no problems. Weird.

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I swear, my cars are like a girlfriend.
Sometimes its a rough ride, sometimes its smooth motorin'.
Sometimes she doesnt like how i treat her and sometimes i dont like how she behaves.
BUT at the end of the day, she loves it when I am inside her.

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'91 850i
'05 X5 4.4i
'09 Clubman S