I have recieved Potions of Cure Serious Wounds from clerics who made them and from stores and loot drops. The ones from stores and loot drops stack fine, but the ones from clerics will not stack with the others.

Bug? NWN issue? Insanity on my part?

Crafted items won't stack with bought items. This is normal behavior. The properties are slightly different in the background.

Ones that you find on monsters or spawns you can sell to NPCs, while ones that are made cannot be sold which is probably why they stack separately from each other.

There are a handful of reasons why potions might not stack, the most likely being that crafted potions don't stack with regular ones. Unfortunately, for various reasons this behavior is necessary.