If you right click a cauldron with any item, it just destroys it rather than use it as a crafting ingredient. Which means that none of the example crafting recipes work. This is why in issue #199 these glass bottles are being consumed but not changing the level of the fluid... because they're being destroyed like every other item that is used on cauldrons.

Bingo, thanks.

Well. Not exactly "bingo". But it got me on the right path.

Either way, duplicate of #199 - but with useful info.