Weapon swap stops working when I enter the boss arena

I am playing a Lightning arrow build and have Lightning Rod on the second weapon swap (which is just linked to the finest weapon slot). As soon as I enter the boss arena on a map, I stop being able to use the Lightning Rod skill.
However, it doesn't always happen, and it seems to be correlated with activating the checkpoint and immediately rushing to the boss or continuing to use the ability to kill other map monsters