My Setup:

04 TL 6MT
Stock head unit and stock amp
Rockford Fostgate 360 (#1)
JL 300/4
Alpine 1000/1
Pheonix Gold Ti12DElite sub
Optima Yellow Top
Focal Utopia front componets
stock center
stock rears

I have the front L/R and SUB connections tapped after the factory amp and they run into my 3sixty. From there the FL/FR wires go into my JL 300/4 and bi-amp the front focal utopias. The sub wire runs to my Alpine 1000/1 amp to power the pheonix gold sub.

Problem:
While the trunk is open the system functions flawlessly. If I close the trunk there is a loud tone from the sub that is constant and won't go away until I turn the car off. Even stays off if I turn just the radio off. I've re ran the ground, replace the amp, tried 3 subs and still have an issue. I'm thinking it's either the 3sixty or factory amp. All the wiring seems fine. If I turn the gain up on the sub amp it amplifies the problem. If I leave the gain extremly low to the point that the sub is almost off I don't get the noise.

Has anyone had this issue? Why would closing the trunk cause this problem?

Thanks

bypass the 360 and see what happens. if you trigger the trunk switch with the trunk still open do you get the same result? or only when physically closed?

It was the stock sub causing an issue. I removed it and no more problem

So you tapped into the stock sub for your signal but left the stock sub plugged in? That will happen since speakers will generate power from their own movement. I have to wonder how the trunk plays into this. Does the closing of the trunk move the stock sub, starting off the chain of events?