I may have stumbled on a solution. There isn't any "SAVE" button for the controller after the new settings have been made. The manual didn't explain anything about that, but on a hunch I pressed "PRO" (for Program) right after I did the last setting. It looks like that is their unwritten way to save the settings, because it has been working the last couple days as it used to work.
Manual is confusing and almost worthless. BTW, it is not a Rainbird; it is a Hunter controller.