Run the following in terminal. This basically resets the Software Update service and allows new updates to flow through again.
sudo launchctl kickstart -k system/com.apple.softwareupdated
Even better, you can make a Self Service policy that runs that (without sudo) with the Files and Processes Payload (Execute Command).
If you are running Nudge or some other update notification, you could also include that as part of the script.
