The water in the bowl of my powder room toilet gets a brown tint after a few hours. None of the other toilets in the house has this problem. I have shut off the supply valve and put dye in the tank and no color got in the bowl and the water did not discolor after 24 hours. It may be unrelated but in the summer a few times I noticed a build up of mildew on the sides of the bowl and inside the lid. That was kind of strange since the toilet was pretty clean. Any thoughts on what might be causing the water to discolor?

Perhaps you have a corroding part (rusty) in the supply line or the tank of the toilet, and after a few hours, the rusty color becomes more apparent? Just a thought. Or, maybe this toilet supply line is not connected to the water softener for some reason - it would be weird, but all I can think of is that there's rust coming from somewhere.