hmmm. ive installed system in all my cars and have never had this problem. however, i had a system installed in my girls car professionally (because its new) and they "pop" when the car is turned off.
if you pull your head unit off, how many RCA cables are there hooked up? does the head unit have a set of RCA cables labeled "sub"? i ask because my subs get the signal from the head unit via RCA cables hooked up to the rear of the head unit to the amplifier, no pop.
head unit > rca cable > amp > subs
my girls car, on the other had, used "high level" input which is (i believe) you tap into the regular speaker wires, then hook that to the amp through the high level input, which then the amp takes the low frequency and runs them to the subs.
rear speakers > tapped wires "high level" > amp > subs