When everything else in this game stacks to 100 maximum before making a new stack, Potency Runes are the only items in the game that stack up to 20 before making a new stack. A lot of us create enchanting mules to hold this unnecessary excess because of this low stack; I could easily get another 25 extra inventory space if they stacked like everything else. Was it an old game design when all items used to stack to 20 and you simply forgot to apply the change to Potency Runes?
Chances are you're going to move this into the Crafting forums, which I have posted this same topic before without much luck on a reason as to why. So maybe before you move it you can give us an answer?