I had this same issue (Nothing would happen on the grid when I pushed the buttons, even if I used a stick), but then it just started working later in the game. Ironically I only found out because another puzzle in the same area broke on me - The silver/gold switch door. No matter how many times I try the correct order, it won't open.
I found the issue with the Bullfrog puzzle, thanks to someone sending me a player.log - the wand needs to be on the same level as the switches, or on a level that you have visited since you loaded the game. I have fixed it locally. I still haven't found what is wrong with the silver/gold switch door. It doesn't rely on any other object, so it's not a related bug.