Windows Updates constantly failing and reverting after SCCM 2012 R2 pushes out updates

Question

Hi folks,
I wonder could anyone help me with a strange problem I am having!
We use SCCM 2012 R2 and I am trying to roll out updates to a Windows 2008 R2 Standard 64 bit server. 
When I deploy the updates to the server they get to the server and install but during the reboot it says Windows Modules Installer for a while then shows the failure configuring Windows Updates, reverting changes screen.
I’ve tried the suggestions of disabling 'Windows Management Instrumentation' and 'Windows Modules Installer' and renaming the repository folder but still no joy.
If I use Windows Update to install the updates the updates do go on but then when I add it to the collection in SCCM to push out the patches it sees the server as if the updates aren’t installed and begins doing the installs. 
After the patches installs using SCCM and when the server is rebooted it goes back into the loop of saying Windows Modules Installer and reverts the updates and strips out the patches again.
I was hoping that when the Windows Updates were installed via Windows Update and once I put the server into the collection to push out the updates to the server it would have shown that the updates are already installed on the server and show that server
as being compliant in SCCM but unfortunately that isn’t happening.
It sights a couple of errors in the Setup event logs on the offending server: -
For multiple patches - Package KBXXXXXXX failed to be changed to the Installed state. Status: 0x80070643
For multiple patches - Initiating changes for package KBXXXXXXX. Current state is Invalid Resolved. Target state is Installed. Client id: WindowsUpdateAgent.
After doing some research,
0x80070643 refers to a .Net Framework issue so I’ve ran a .Net Repair tool but that didn’t work either so I’m running out of ideas so any help would be greatly appreciated on how I can get this sever updated using SCCM and showing as compliant.
Thanks,
Bonemister

Answer 1

Hi Torsten,
Thanks for your reply!
I was afraid you were going to say that as it just doesn't make sense that when I install the update using Windows Update via the Ire-nternet and when the install and re-scan no updates are required.  It is only when I ask SCCM to check for patches
that it sees updates are missing and installed the updates before the OS reverts when.
Is there a way in SCCM to remove the record of what patches have been installed onto a particular server?  I tried deleted the server out of SCCM then applying the Windows Updates via the web then added the server back into SCCM and see did it pick
up the newly installed updates on the server.
The thing is I don't think that WindowsUpdate.log will show any failures as Windows update is showing as no more updates required.  It is just when SCCM installs that patches that the problem happens so that is what is leading me to think it is an SCCM
problem.
My main goal is to get the updates into the server and for it so show as complient!
I'll check back through the even logs again.  Are they any SCCM logs that show patches failing to install and why?
Thanks again,
Bonemister