If you don't get better results with a different Y cable, my thoughts are that the long RCA cable up and over the top is picking up noise from electrical along the run.
It may come down to you needing to replace that RCA and run a Balanced XLR cable.
I would also try if you can, instead of using the splitter, just run one cable to the close sub and run the long cable out of the Low Level Out from the first Ultra to the other sub... daisy chain style, if its at all possible.... worth a try