There are several factors that affect pH, and before jumping to conclusions you should consider all of these.
First, what is the pH of your source (tap) water? When you test pH in tap water, there are a couple things that might be affecting it. Primarily here is dissolved CO2. There can be a lot of CO2 in tap water, which is not dangerous but it might affect the pH test by making it seem lower. CO2 dissolved in water produces carbonic acid, and this lowers the pH. So let a glass of fresh water sit 24 hours, then test; that will be a more accurate reading.
Water authorities sometimes add chemicals to raise pH if the source water reservoir is acidic. They will tell you this, probably on their website. Probably not relevant here, but good to know anyway.
Second thing, pH is closely tied to the GH and KH. The latter (also called Alkalinity) works to buffer the pH, preventing fluctuations. All three parameters for the source (tap) water on its own need to be ascertained. Check the website of your water authority. Post the GH, KH and pH they give.
Third, aquatic plant "soils" often impact GH/KH/pH. The info on the website of the manufacturer should mention this, either way. Check that.
Fourth, the seiryu stone...online info says this can affect GH and pH by raising it minimally. This may or may not be an issue, we will know better when the other factors have been sorted out.
Fifth, the substrate as already mentioned, what is it composed of?
My final summary comment is that water chemistry in an aquarium can be incredibly complex and involved. We are dealing with natural processes, meaning what play out according to the laws of nature. In the habitats all of these factors are what we may term very stable and permanent for the most part, so things don't change much. But in the veery minute confines of any aquarium the biological/chemical system can be significantly impacted by something quite unsubstantial in itself, but when everything works together cause this or that. It is always safer for the fish to have these influences/factors as few and minimal as possible.