It sounds like you are getting way too much input into your amp.
Most amps should never get more that 8volts (RMS) into the RCA inputs.
By sending 22 or more volts you may have damaged the input section of your amplifier -----however JL Audio amps are built pretty well so you might be ok.

I would suggest installing a hi-low converter between the outputs from the factory subwoofer and the input on your amp.
Other than that go to a shop and have them check it out.
Sounds like an easy fix.