Sorry for the late response. So far I cannot officially find where the problem noise is actually coming from. I enabled the water hammering feature which I do think quieted down the noise a bit, but it did not make the noise go away. I crawled down into my crawl space to find the source and to my dismay couldn't find it. At this point my best guess is that its either the backflow preventer, which I have yet to locate, or it's just the noise my system makes when the water is flowing through the valves. I'm at a loss.
Good news is the Rachio works great and I have no complaints there! Now if I can just fix the noise...