Limit 1 runes prevent weapon swap if both weapons use the same rune

Is it intended to globally have the rune limited to 1 or should it be limited to 1 "active" rune? Both weapons are not being used at the same time so only one rune is "active" at a time. Not sure if this is a bug or deliberate.

For example, if you have the 50% increased attack damage against rares & uniques rune in both weapons for set I and II, it completely disables the second weapon from being used and skills being assigned to it.

Having same issue here... kind of discourages you from using weapon sets. This must be a bug?