I'm guessing, that there is a wire shorting out somewhere. I saw this in my buddy's house stereo before. The stereo would go into protection mode after a certain volume. Turns out one of the wires was getting shorted out with a speaker stand.
Check the wiring again. Maybe something pierced the wire like some sharp metal.
Also, the speakers and head unit may not have matching impedance, but that doesn't say anything for the window up/down thing.