In 2010, measurements of energy levels of muonic hydrogen, an atom with a proton nucleus and a single muon orbiting it, instead gave the proton size as 0.842 ± 0.001 fm. The muon is essentially identical to the electron, but 200 times heavier. As a result it orbits closer to the proton, and can determine the proton size more precisely. The collaboration published an improved, consistent result in 2013.
These matters are extensively discussed in a Workshop on the Proton Radius Puzzle in Trento, Italy in late 2012 and in a review paper by Pohl, Gilman, Miller, and Pachucki. The inconsistency is now at about the 7σ level, and is attracting a lot of attention.