If you have a pump fed system there may be suction leaks on the pump intake line causing the pump to “surge“ or not keep a steady flow of water needed to keep the valves disc depressed and on one zone. Diagnosing, locating and repairing a suction leak may require professional assistance.
Or if the pump is located more than a few feet from the water source the disc inside the valve may pop up and down skipping zones as the supply line fills purging air. Move the indexing valve closer to the water source, the electric control valve or pump closer to the indexing valve or pressurize the supply line.
Also, if the valve is not installed at the highest point of the system there may be back flow entering the valve after shut down which will cause the disc to skip as it is pushed against this back flow by water coming through the inlet during start up. Install a check valve on any outlet that has zone piping higher than the valve.