Yes, the sub is on the right side compartment.

I am betting on a bad connection somewhere. You have the "New Gen" radio in your car and those are not prone to failure. (Not to say that they never fail, but it is not a high failure item.)

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2000 E38 750iL Highline Edition, Upgraded with the lastest 2006 X5 Electronics
MKIV Navigation, 16:9 Display, Bluetooth, TV/Video with Backup Camera, Sirius, and Aux Input