w/o knowing the exact specific wires that you tapped into...
I have always took my signal from the rear door outputs off the amp, not the head unit, this is a full range signal. There must be something the head doesn't like about the low level outputs having it's resistance load changed.

Another alternative you could try, slightly unorthodox, would be to leave the outer shield of the RCA unnattached as how you got sound w/o interruption, and ground the outer shield of the amp's rca. Simple to just take a piece of ground wire and try this quickly. Do not worry, no harm can come of this, but it may have no result also.