Water sprinkler problem

We've had our automatic sprinkler system for almost 20 years. There has been small problems, including valves that won't shut off and I have always managed to find the source of the problem and repair it. But this time I am stumped. It seems that the controller is turning on more than one zone at a time. For example, zone one turns on, runs for the 5 min interval its programmed to do, then turns on zone two without turning off zone one. It's not a valve problem because zone one can be turned of manually at the controller. If the valve was stuck in an open state it would not respond to the controller at all. This started happening after I interrupted a cycle once changing the length of time midstream and it is the same zone that is now not shutting off on time. Any suggestions?