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Could you clarify the run time you are referring to: is it the program run time, or a manual / run-once program run time? Note that for watering percentage to take effect, a program needs to have the ‘Weather Adjustment’ flag turned on. It might sound unintuitive but the idea is that any adjustment (whether manual or automatic) is considered weather adjustment. And some programs may be for running lights and stations that should not be affected by weather, so the flag is provided as an option.
Watering percentage does NOT apply to manual or run-once program as these are considered manual overrides.