I'd start by checking all of the connections from the head unit to the wiring harness...especially the ground and power wires. Make sure everything is tight. Also check the RCA connections. Look for the voltage regulator and check it - the Shaker system requires a +5V signal turn on, and aftermarket units use a +12V signal. The "fix" is a RadioShack voltage regulator wired in-line on the remote turn on wire from the HU to the Shaker wiring - it should be the blue/white wire on the HU. It has 3 connections - in, ground, and out. Check all of those - it sounds like the Shaker amps are losing the power-on signal.