[Yggdrasil]

One problem with dealing with hydrogen is that, because of its small mass, it behaves quantum mechanically (e.g. it is often found to tunnel through barriers) and the mass of the hydrogen atom will have significant effects on the behavior of the molecules that it is in (e.g. it significantly changes some vibrational modes).  Protonium and deuterium likely have slightly different hydrogen bonding behavior which would account for the difference in boiling point.