Timers with a diaphragm need a minimum flow and pressure to operate correctly, usually 30 gph and 15 psi. Water surge on start-up can "fool" the timer into opening but once the initial flow and pressure drop, it will not close when scheduled. To test this, open the end of your mainline and, if the timer shuts off when it is supposed to, you know you do not have enough water flowing through your system. If you have several small zones, you might consider consolidation to fewer, larger zones to increase flow. Battery timers can also use a lot of power to open and close the valve inside, be sure that your battery is fresh and is an industrial strength alkaline battery.