Probiotics do kill candida…the lactic acids break down the walls that protect candida. Boulardii also produces lactic acids which cause the same process, just at higher amounts.
Its hard to say whether you are experiencing die-off or not. Headaches can be related to inflammation of the gut, pains/aches can be tied to dehydration, tiredness could be related to poor sleep, etc.
You never got die-off or any of these symptoms from antifungals?
You could have something similar to candida such as SIBO, h.pylori, strept, etc.