While I don't know what takes precidence over what, but I do know that you can't have runes of the same type (ie: Vigor or Strength or Axe, etc.) equiped at the same time. It doesn't matter if its a Major, Minor or Superior rune, if one rune is applied, you cannot get the benefits of another rune.
As I said, I don't know if the first rune is the only one applied, or if its the last one, or if its the "better one" or whatever. I'm guessing its the first one that is applied is the one that counts.
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