No idea either, but I'd bet I've seen them as far back as AOS. Digging around a bit,
the old Bloodtile site, back in 2004, said these came from a bug I do remember around that time. It was around the same time as when carto was a big money maker, if I remember correctly. It was possible to glitch a runebook such that you could remove infinite numbers of runes from them.
According to Bloodtile, it looks like there was a variation on that bug where you could remove runes from the unused slots of a runebook as well - and from those, the 1-stone ones were the runes thus created. (Fixed by Publish 27). At the time, new runes from NPCs were labeled "An unmarked recall rune", vs the modern "Recall Rune". When you marked a rune, the facet was bracketed at the end of the rune's name, ex: "a recall rune for Britain [Felucca]". I'm pretty sure all of the 1-stone ones I've seen also have that [Felucca] indication on there, something like "An unmarked recall rune [Felucca]".