Well good news is that a clean install has fixed the missing registry entries problem. All windows updates now applied successfully, allthough KB2872339 was downloaded rather than KB2859537.
I have been reinstalling all of the applications previously present and checking the registry every so often, but so far nothing has removed them. Obviously in 2 years lots of applications have been installed and removed though so could have been one of those
or simply a corruption at some point, but it does look far from random as both registry entries were missing, but those around were unaffected.
So message for MS is to display or log some sensible error message rather than casing a BSOD please.