How is it wired, I belive the OEM sub uses the high level output form the stock radio & converts it internally in the amp in the box.
Where is box grounded? you may need to run a 2nd ground to back of radio. try disconnecting inputs to sub & see if it goes away.
If it does then there is a gnd difference between deck & sub amp. if noise is still there, then try a different power source like a battery thats not connected to your car. (I use a power supply), just had an install this weekend that was having wierd problems with the the stock electrical system. External power source can help toruble shooting faster.
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