I get the same thing on my Aquarite (about 7 year old now). When you turn the power on at the timer (either manually or when timed), the white Aquarite contoller box CLUNKS, pretty close to a bang, as if someone hit the back of the unit with a small hammer.
Last year, I was able to reduce the noise considerably by rewiring the ground line to the controller, I may try it again this year - actually replacing all the wires. I'm thinking that the contacts get gummed up somehow over the winter, causing the clunk, but I don't really know for sure. The noise is loud enough that I think whatever is causing it may be visible if I remove the faceplate (using extreme caution!!), but I haven't gotten around to it yet.