New runes were explained on last big update patch info...
There are 2 types of basic runes, the ones you get by drop from boxes, promotions, stores, etc AND the ones you get from lvl up achievment quest.
Same icon, they are used for the same and the only way to know the difference is to read the description, as the QUEST ones ends the description with brown message that reads "UNABLE TO TRADE"
Think of tradable ones as "RUNE A" and quest not tradable ones as "RUNE B"
In order to learn skills that needs 4 runes, you need 4 RUNES A or 4 RUNES B, but you cannot mix them, so you cannot learn the skill using for example 1 RUNE A + 3 RUNE B, all the runes must be the same type.
Why the system is implemented this way? No idea, but probably made by the same "GENIUS" that stated that a wizard weapon must be turned to warrior weapon with red libra in order to use Heavenly Scroll Enchant Weapon to be able to enchant over +7... so the scroll can be used on a warrior weapon +7 but not on a wizard weapon +7
Again, why the system is implemented this way? That is because L2 works in misterious ways that even God does not know