My JVC headunit cuts out on the factory speakers in my car. Its like a cd that skips, but it does it using the aux plug also. Only the factory speakers stop working though. The subs keep playing. The pause is only for a second. It seems to do it more when I push the break, but I'm not sure. I can't find anything that makes it happen all the time. What could that be?
Are you giving it enough power? I.e. are the power cables big enough? What JVC head unit is it? And how long has it been doing this? The internal amp might be going bad.
Also, check your speaker wires.
My guess is you have some speaker wires that are touching each other and causing the internal amp to short out.