Sometimes funny things happen when you start digging deeper. I stumbled across a brief note by Prof. Haverfield in the Proceedings of the Society of Antiquaries of Newcastle-upon-Tyne for 1911-12, p. 184:
"...[The standing milestone] is often called a Roman milestone as the Romans left it, and tourists (as I know) often admire it as such. Whether there remains anywhere in Europe a Roman milestone which still stands erect as the Romans left it, I do not know. Chesterholm, at least, cannot boast of that glory."
Prof. Haverfield points toward the smoking gun in Horsley's 1732 Britannia Romana. I just read the passage myself, and it seems pretty clear. The following, from p. 228 of Britannia Romana:
"Near Little Chesters, there are some of the milliary stones, which are said to have been erected at the end of each mile upon the military ways, from whence the phrase ad tertium, or ad quartum lapidem. One of these is thrown down, and lies under an hedge near the rivulet, a little east of this station. And about two miles west from the station upon the common there is another. But the most curious one is standing at about a mile's distance or less from this place to the west. The military way that passes directly from Walwick chesters to Carrvoran is here very visible, and close by the side of it stands a piece of a large rude pillar, with a remarkable inscription upon it in large letters, but very coarse, BONO REIPUBLICAE NATO. No doubt this was a compliment to the emperor then reigning, nor is it an uncommon one. I don't find this has ever been taken notice of before."
The stone a mile west of Vindolanda with the inscription was noted by later 18th C antiquarians. Anthony Hedley also noted it in 1822, saying it had recently been destroyed, leaving just the stump in the ground (the stump still visible today when you first turn into the Stanegate on your way to the site).
The milestone that we see standing proud today behind Vindolanda's museum seems to be none other than the one that Horsley saw in the same location, lying forgotten on its side. So who put it back up, and when?
I have wondered about that milestone too. If the course of the Stanegate is being sought in the fields to the north of Vindolanda, and the farm track passing the north wall of the stone fort is just that - a farm track - it is surely doubtful that this Milestone is in its original position? It is a shame, because the idea of having two exactly a Roman mile apart is so tempting.
That wonderful tome "Frontiers of Knowledge - A Research Framework for Hadrian's Wall" mentions the finding, in 1885, of 5 complete and 2 fragmentary milestones at Crindledykes, just east of Vindolanda. I wonder why they were together and where they are now?
It is also interesting to note that there is at least one other Roman Milestone believed to be still in situ. It is at Temple Sowerby on the A66 in Cumbria. See http://www.stone-circles.org.uk/stone/templesowerby.htm for a picture and more details. I'm kicking myself because I must have driven past it last Saturday and forgot to look out for it.