That's an interesting problem, I don't use tap directly myself. How much water do you need for the reservoir? There are the water machines (usually at grocery stores) that filter the water. It's usually $0.25 a gallon, you just fill your own containers. You may give that a try, and see if the problem disappears. Not sure about fluoride, but chlorine is no good for plants. I believe it's a form of bleach (as in chlorine bleach), and bleach does loose it's potency over a short time when diluted. So that would certainly make sense, but I don't know how much it affects the pH.
You can also place some tap water in a jug and test it right away from the tap. Then check it every day for about a week, and see if the pH changes like you are experiencing in the hydro system during that time. The local water company can tell you what, and how much is in the tap water. But it would be local because it varies a lot from city to city. But none of the chemicals that the water company uses would be any good for the plants. I would defiantly try to get some better quality water regardless.
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