Auto-sweepers no longer supplying bottled liquids to Bottle Emptiers

This was never a function in the vanilla game; sweepers could only pick up bottles of metal, not of any other liquid. Check your mods to make sure they're working properly; No Manual Delivery in specific has a function for this that has to be explicitly enabled.

I swear Magma used to work... was there a reason for why some bottled liquids work and not others?

Functionally, it's because molten metals are tagged as Metal which is a category that is included in what conveyor arms can pick up. Whether this is by accident or design is anyone's guess, though given how most niobium volcano tamers depend on it it's not likely to change any time soon.