I think it was spell 3? If it wasn't timeout after all, then I guess I just wasn't paying enough attention to where I was firing, sorry. Right, so I tried the game again, and it's because I didn't realize bomb invulnerability meant the boss became invincible too. And during that spell, I bombed a lot.
Oh, forgot to mention, I think the menu is bugged. I tried "Restart from beginning" during gameplay and while it does restart, the game seems to remain irreversibly paused when I do that, even if the menu is gone. You probably already know about this, but I just wanted to mention it just in case.