The only ways that GH and KH can rise are either by having a lot of evaporation so that things dissolved in the water become more concentrated, especially of the water just is topped up rather than doing water changes; or by minerals getting into the tank from a non-water source. And as you say, the usual suspects are the substrate and decor.
To check the substrate, if you have any left over (or remove some from the tank and wash it) put some in a tub of water and leave it for a few days. Set up a second tub with just water. After say a week, test both tubs for GH, KH and pH. If they are the same, it's not the substrate. If they are different, you've found the culprit. And do the same for any rock decor.
Do you add anything to the tank other than food and dechlorinator eg plant fertiliser? If you do, have you checked the ingredients?
