I have a 500/1 Slash series amplifier hooked up to a pair of 12" infinity Kappa perfects. I have a factory dash unit still in a 2007 Lincoln MKZ so im using the converter that converts the speaker wire to the plugs that go into the amp for audio. I listen to rock music so my amp is only turned up 45-50% and sounded GREAT. The problem just started about a week ago, whats happening is at low low volumes i can hear the subs going and right when i go to turn the volume up the subs cut out the green light on the amp turns off and the red thermal light will flash once every 10 seconds or so. I have checked the connections in my sub box and all the wires connecting to the amp, and also battery and ground. I cant seem to find out what is up.

What may of happened if that you got the lacquer finish on the electromagnetic wire to heat up and come apart. At low volume they will still have an electric connection. Because the wire physically came off from the inner housing of the voice coil it is in contact with the side wall of the speaker magnet and is proned to causing a short between coil sets. Your probably running subs with a 4 ohm impedance and when your coils short it acts more like a 2 or 1 ohm speaker. This is similar to whats called a dead short. Since the Independence is dropped to 2 or 1 ohm it is the resistance equivalent of having 2 or 4 subs attached to your amplifier which caused the final transistor bridge to heat up and it can get hot almost instantly. Check your amps outputs individually on a single speaker that you know works perfectly. If your amp does not trip the thermal protection you most likely cooked a speaker beyond usable condition.