I never though of this before, but is it's possibly that latinum is a living organism? A chemically complex semi-gelatinous organic lifeform.
A small colonies of it lives inside the gold box that holds it, maybe it extremely slowly consumes tiny quanities of the gold, over the course of centuries. It reproduces (by division) only in a small natural environments locate upon the boggy Ferengi home world. No one has ever been able to duplicate this exact environment, scientists aren't sure why.
It's a popular theory that latinum can not be replicated. The replicator has been shown to have difficulty with producing living tissues and bodily organs.