Well I've never used it but my guess would be that some enemies are resistant to it. Also a lot of attacks that look like magic aren't. This is really dangerous. I gave a boundary rune to Isabel to fight one of the minibosses at the end dungeon because it had this big laser attack that hit everyone, but it ended up doing over 900dmg to her because it was apparently a physical attack. That theory doesn't really work in this case sense you know their casting earthquake, but maybe for other enemies thats the problem.