Vibration In Subs

I have the Shaker 1000 system. Just about 58,000 miles on my car.

Driving home from work, noticed I was getting this bassy "wup wup wup wup", etc. sound like maybe air bouncing around in the cabin of the car. Turned volume down and turned the AC off and it seemed to stop.

Later on, left my house to go somewhere else and it started again, but worse this time. I didn't even know what it was. Was it my exhaust? I definitely knew it was coming from the rear and the likelihood that it was related to the subs was quite large. I pulled over to the side of the road, opened the trunk, and I could see the speaker kicking/vibrating nonstop. It wouldn't go off unless I just turned the whole sound system off (switching the shaker from "On" to "Off" in menu didn't help). It sounds a LOT like my exhaust, vibrating at a similar frequency, but much louder.

Anyone know what this is? I looked at the speakers, they look good. All the solder connections inside the amplifier look good as well. I was reading up on "ground loop isolation" and it seems like it could be the culprit. If that is the case, why wouldn't Ford install ground loop isolation in the first place?

Did some thinking within 24 hours of my first post and I realized that I do keep a set of jumper cables in my trunk, usually wedged between the outer trunk edge and the actual sub cabinet; that is a lot of copper wire and conductive material, so I have to wonder if the magnetism was messing with the subs at peak volumes. It's been a week and I have kept the jumper cables isolated from the speakers. I haven't had an issue since I wrote this email...not sure what it was. I will update if it happens again.