You might have them in your rune pouch, you could also just put both nature and fire runes in your rune pouch and it will use that instead.
I did some changes and should fix it in V1.01
You can use a trident or any other wep with a built in spell and have it equipped at this point.
Bone staff being the best by far, just like other bone weaponry against this boss So once you get a spine drop just get it asap ^^
Khal Scurrius updated to V1.01:
- Changed some of the banking logic when being out of the instance
- Fixed issue with rune pouch check for alching runes
Live soon!