First watering at night is not a good thing. The plant is in the cooler night air with no way to dry off. You are inviting plant diseases to move in. The best thing would be to set your system to come on around 6 AM. That is early enough that most people won't be up and in the garden but late enough that the plants will soon dry. A note to renters should solve the problem of early risers. Early morning watering will keep the flowers from freezing in the fall too.

You may have a case of blight starting. I would remove the brown leaves even if you have to clip it down and dispose of them in the garbage. If it is disease it spreads from leaf to leaf with water droplets that carry the spores. You certainly don't want it spreading to other plants

I cut back many of my sprawly geraniums in July and they come back with fresh new leaves even if they don't flower again this summer. Usually I cut back all the sprawly, flowering stems and just leave the healthy short-stemmed leaves at the base of the plant. It sort of depends on the exact variety that you have. The plants then look much tidier and healthier without those ratty leaves and straggly stems.