lol, I am having exactly the same problem ....do you have an Alpine head unit?
so you have run 2 sets of RCA's, 1 for channels 1&2 for the splits and 1 for channels 3&4 for the sub?!
first try changing the cross over settings on the amp using a small screw driver or your finger nail. Also there should be 2 HPF/LPF (High/Low Pass FIlter) switches, make sure you have it set to high pass for the splits and low pass for the sub
I have mine setup like this with still a few problems, I think my problem is the RCA connections in the back of the deck.....
have fun!