Looking great!
I'm also getting a glitch where the boss stops creating it's hitboxes if you restart the game a few times.
Impossible to say for sure, but this suggests to me that either the boss itself is not being destroyed and reinstantiated or something to do with the hitboxes is being stored in a place that isn't being cleared out before each fight. Generally, I'd expect this to be the result of stale state.
Good luck, keep it up!