I might take some of the substrate, isolate it in a plastic tub with tap water, set a cup with plain tap water next to it and monitor the GH in both. If it's not the substrate, there must be something else causing the fluctuation. Repeat the test with other objects until you find it. Without finding the cause, your tank is always bound to be 'different'. Yes, I've been (am still?) there!
Topping off with tap water could do that, but that would have to be a lot of topping....what, likely 3-4x the water volume. Certainly possible, but somewhat extreme.