Why Sir. Our support team is really responsive so I'm sure they can help figure this out. I'm happy to help as well. Based on what you described, I just need a bit more information.
First, have those two zones always run together from the start? Or did they only run together briefly? If it's the latter, check if you have the water hammer minimizer enabled. If they run and shut off together, it's possible the wires for the two zones got connected to the same terminal.