Try adjusting the float settings. I had one that did this same thing because the float was too high which allowed more water into the tank and it slowly trickled into the stool (nothing you can notice) and then when the float went too low, it would refill.
If you simply adjust the float to be a little lower, it will cutoff the amount of water in the tank and should fix the problem. This is assuming you don't have a leak that you haven't found, if it still continues, or gets worse, you might still have a leak.