I'm not reading all the posts but did you try to swap the amp with something else and see if it does the same? Faulty/failed components in your hardware(such as bad resistor/cap in amps or headunits) can cause more strange problems than I care to type out.
As far as power cables... you don't need a negative power cable running from your front battery(yet), because your car chassis can easily take the current load from one Audioque 2200. People only run multiple runs of power wires if they have extreme levels of power(like over 4000 watts RMS), a poor chassis or lack of it(such as vehicles sitting on tubular frames) or they're in bassrace or some type of SPL league and are only allowed to have one or two batteries in the vehicle. Thick power wires can cause interference with sensitive electronics in the car so do keep them away from all the modules and chips. I suppose it doesn't hurt to have more runs of power wires but it'll definitely hurt your wallet, weigh down your car and you'll have to find places to hide it.
Also you're definitely doing something wrong if you upgraded the wires from the alt to your battery and ended up draining it. Take some pictures and let us see your setup, because Jesus isn't gonna help you install a stereo.