I had this problem with my RSbot alcher, it only equipped the arrows when I lagged though. Nothing you can do about it, i'm afraid, unless you equip another sort of arrow so when it misclicks it starts alching the others.
Use iPHG's Alcher, it's free and works flawlessly. If you lag and it equips arrows, it unequips them for you. I'm currently alching rune arrows myself at sw bank so you should be good to do the same