Not sure if it's a permanent fix, but it's working. Oh Yeah!
I realized that there was no clicking noise when I pushed the AUX2 button (which controls the pump for my polaris). But when I pushed AUX1 button their was a click. So I figured since AUX1 wasn't controlling anything, I would just switch the wires (after turning power off, of course). And it works.
Just got to figure out how to program it. When I go through the programming menu it doesn't give an option for AUX1. But it works when I manually turn it on. But, it works and I gots a clean pool again.