try a different amp. any amp. just give the sub whatever you got. try and run them seperatly.
also might wanna get a DMM and see if there is some kinda voltage increase\decrease... put it on the battery with the volume at normal, and watch it when that noise comes out. does the voltage (should be ~14) go up or down drastically?
did you upgrade the big 3?
how thick is your power wire?
what fuse do you have on it?
how are the subs wired and whats the voice coil config?
have you tried another pair of subs yet?
can you hear it through the stock speakers?
try another set of RCA (even though they SHOULD be ok).
When I first installed my system, the inline fuse under the hood was a bit small for the fuse holder, and the amp would lose power + turn back on/off at random, sometimes making a popping noise. Does it do it when you are driving or sitting still ?