“Skipping” to next zone on a quick run doesn’t honor cycle soak and properly cycle index valve, how can I fix this?

Between the weather skips and me being away from home and thinking I’m manually watering the grass with a quick run, but come to find out if I “skip” a zone the controller isn’t properly honoring the cycle soak and actually cycling the index valve resulting in a single zone being watered the entire time… my grass is dying! This controller was suppose to simplify my life and instead it’s killing my grass. How can I fix this?