The gain knob isn't a volume knob so "turned down" doesn't mean much if you have an extremely strong source signal. Also when you say you have a rattle from the sub itself, do you mean the driver or vaguely somewhere inside the enclosure? If it's loud enough to hear over the music I'd recommend taking the subwoofer out of the enclosure and playing it VERY softly to see if you can tell what part of the driver is effected if any. A large number of things can cause rattle or noise from a driver, but most of them are going to be loose parts inside of the enclosure such as a basket plastic shell that's fallen off, a wire interacting with the cone, messed up voice coil/spider, or any number of other things.
If the driver is okay at low volumes and outside of the enclosure then don't go back to listening to music until you set up the amp properly either using ohm's law + a multimeter + 0db tones or just an oscilloscope/dd-10. Speaking of your amp, you listed it as Kicker but that model number corresponds to a Hertz amplifier. Are you sure it's Kicker?