the only thing I can think of is your overloading the input of the PA system. I was using an active direct box (had a battery) and an active bass. I got all kinds of crazy noises, tried a passive bass and it went away but it was not the bass I wanted so I went to a passive direct box.
my suggestion is to lower the volume of your amp starting with the pre-amp (called gain or pre-gain)
Try a direct box and not using the amp.