I believe there is either a hidden weighing for Rune of Havoc, or it doesn’t work on crafted axes.
I used about 15 Runes to try to hit a Tier 7 added Spell damage on several one handed swords. I made sure to even out the non tier 7 afixes before use. It moved, but never on to the crafted added spell damage.
So it’s one of 3 possibilities.
a) It doesn’t shuffle properly onto afixes that you craft on to the item,
b) There is some hidden weighing
c) I am unbelievably unlucky