I don't remember reading anything that implies flask logic is buggy. Certainly, it would require tweaking to tailor it to your build, just like regular skills would.
Looking at the AHK script, I'm not sure I see anything it does that EB can't. Seems to be just basic logic to pop a flask when you drop below x% health. EB can do that, and also add in other conditions, like only use it if you're surrounded by mobs, or fighting magic/rares/uniques.
What I'm wondering, is if there's any way to keep track of incoming damage, and only use the appropriate flask if you're taking that damage type, to avoid wasting Resistance/Armor/Eva flasks on the wrong damage type and then not have it when it's really needed. Not to imply that should be a priority feature.