Is the battery still good? I'm torn on which direction to send you. I want to say there's a problem with the power supply side of the controller. Supposing the timer is plugged into an outlet that is controlled by a light switch. Someone turns it off and on, the controller will flash if the battery is dead. Or any other power supply problem. Loose connection on the transformer for example.
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Could be a wiring problem where two wires intermittently touch or are loose. Check all of the splices. I had a controller that would blow the fuse every few months. I finally put a slightly bigger fuse in the controller because running a new wire was too difficult. That was 7 years ago. The controller's still working.