So today I saw a dozen of computers which failed updates evaluation in a SCCM 2012 R2 infrastructure. Inspecting SCCM client logs revealed a "Failed to run BeginSearch on WUAgent. Error = 0x80080005." in WUAHandler.log. This seems to be a generic Windows Update error which means that Windows Update (wuauserv) is not started. After starting the service update scans succeeded and updates installed without any problem.
Of course you should try to find a reason why Windows Update service was stopped, because this is not a normal Windows configuration.