SCCM not synchronizing with windows updates
I have a SCCM server installed on site to deal with client and server machine patching. After the last patch Tuesday I noticed that the windows updates under Software Updates had not been synchronized with the latest updates. To dig deeper into this I navigated under System Status – Site Status – <<site name>> -Component Status and noticed that the SMS_WSUS_SYNC_MANAGER component was in a warning state. By right clicking and selected Show Messages – All i was able to see a bit more information:
The entire description is as follows:
SMS WSUS Synchronization failed.
Message: Thread was being aborted.
Source: Microsoft.SystemsManagementServer.SoftwareUpdatesManagement.WSyncAction.WSyncAction.SyncUpdates.
Seems strange that the thread was being aborted so I decided to have a look at the good old Application event viewer to see what was going on at a similar time. I found that the SMS_SITE_BACKUP component was running a split second after the SMS_WSUS_SYNC_MANAGER component which was causing the SMS_SITE_VSS_WRITER component to stop the SMS services as part of preparing for backup (wow that’s a lot of components in one sentence!)
I then changed the schedule start after property for this back up component task by navigating to Site Management – <<Site Name>> – Site Settings – Site Maintenance – Tasks – Backup ConfigMgr Site Server Properties and set the Schedule to run at a time that doesn’t conflict with the synchronization (just an hour later than it was).
This solved the issue and updates are synchronizing happily again now 
Hopefully this can save you some valuable troubleshooting time!