My car stereo is pulsing, whats going on?

I recently hooked up a sub/amp system in my car. Everything was working fine and I used a stand alone battery system off a new battery as to not overdrain the car battery. I also have a seperate switch the turns the battery on and off to not constantly drain the seperate battery. Then all of a sudden I turned it on once and the subwoofers started pulsing like a heart beat one after the other. I then investigated the situation and took everything apart and put it back together. Then turned it on and it all worked again. Then out of nowhere again it started pulsing and I couldnt figure out what I did. The quality of all the electronics is great and the condition is impeccable… Please Help

maybe spark plug wires could need a noise filter/suppressor

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