I had a similar issue with Mana Potions. Saving and reloading fixed it for me. Haven't tried Purity Potions yet. EDIT: To be clear, I still encounter the bug whenever I brew Mana Potions and am forced to save/reload in order to make any Mana Potions in my inventory stackable. EDIT #2: Actually, it now seems like you cannot stack items from before and after a save+quit/restart together. Probably due to the new inventory save file system.
Sometimes when you load a game, any new potions you pick up don't stack with the old ones in your inventory, it happened to me everytime I loaded a game so far and goes for just about all potions not just purity and mana.
I got to thinking that maybe the devs made potion stacking scalable to your level but I'm having many problems with alot of potions not stacking then stacking on another play session
I have this problem, and it is very annoying: if I have some Aqua Vitae and, after loading the save, I distill some more Aqua Vitae, they don't stack.