fsa3, you are not alone. Alot of ppl including me with my new BOX experienced such a problem. There is two things you can do.
1) go to Radio Shack and get the ground noise filter thing ($14). There also have a battery noise filter too. I Use the ground noise and it definetle killed the noise from the engine but i still have just a tiny bit left. I think that is comming from the battery so i will have to get the battery one too to test my theory.
2) This is where the problem is prolly. Try using proper wires in ur box. Take the box apart and make sure EVERYTHING is grounded properly. You will be supprise to find out that something isn't grounded as you thought it was.