dusty,
Switch your amplifier crossovers temporarily from highpass to fullrange on the other amplifiers/channels to verify the noise is not in all amplifiers. If its only in a single amplifier then the turn-on/off delay circuit or input muting circuit is defective in that particular amplifier. If it shows up in all amplifiers then its a problem with one of the source electronics or your wiring scheme.
At the root of the issue is that an amplifier input should be automatically muted so that it doesn't remain on to reproduce the sudden shut-off or power-down of the source electronics. If you think about it, its pretty easy to diagnose the cause by the process of isolation and elimination. You can also use a manual switch to temporarily and manually control the amplifier turn-on/off circuit and the sequence relating to the source electronics powering down.

David
Earmark Marine