The first thing that I would do is double-check your cable routing. Make sure that the tuner interconnects are well away from the phono interconnects. Phono gets the largest boost in signal strength in a system so any stray noise will get boosted along with it. It's also especially important to keep phono interconnects away from power cables for the same reason.
Rogue Audio Cronus Question
I'm just getting used to a new(used) Rogue Cronus (not the Magnum) - and I noticed that if I leave the tuner on (Aux 1) while listening to the turntable (Phono), some faint music from the tuner comes out of ONE of the speakers. It's in phono mode, and obviously I can get rid of the sound by simply turning off the tuner, but why would that happen, and how can I correct? Thanks.