I bet I know exactly what it is. It's an aftermarket radio, right? When they installed it, they used the power antenna output to power the factory amp's turn on input. Take the radio out and see if the blue or blue/white wire is used coming directly off the aftermarket radio. They should have connected the radio's Blue/white to the jeep's harness, but they probably used the solid blue wire instead. This would only let the factory amp work when the stereo is on the radio source, not AUX or CD or anything else. You can confirm that this is what happened by putting a CD in and seeing if the sub works then, if it doesn't than they hooked it up wrong.