We have two freshly built Server 2012 R2 machines (Standard with GUI). In both cases, we installed, ran Windows Update until it converged, then scanned with Protect and applied everything it wanted. Protect says MS14-A07/Q2973351 is needed because:
The registry key 'SOFTWARE\Microsoft\Windows\CurrentVersion\Component Based Servicing\Packages\Package_for_KB2973351~31bf3856ad364e35~amd64~~6.3.1.0\CurrentState' does not exist. It is required for this patch to be considered installed.
but the install fails. Windows tells me that 2973351 is installed and the patch says not applicable if I run it manually
The above registry entry does not exist, but there is an almost identical entry with 6.3.2.0 instead of 6.3.1.0.
If I uninstall 2973351, reboot, and install again with Protect, I get the registry entry you expect and a scan says I'm up-to-date.
Uninstall again, then reinstall with Windows Update and this time I get 6.3.1.0 (the value you expect).
Microsoft, what are you doing???