I have been encountering the updater not enabling all updates to happen, there would be updates that would not be checked and can’t be either. One that just happened is with VirtualBox, it will not update to the latest. I have purged the system of VirtualBox installation files and went to install the latest and it is just reinstalling the original that I had on my system before the header was updated.
are the updates being held or do they just not show up
If « being held » then probably 
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They are being held when I go look in the terminal for the sudo apt update, but for the software updater they show, but are not checked and can’t be either.
As @Coeur-Noir said, the withheld packages are so-called phased updates. The progress of phased updates can be seen in a report called Phasing Ubuntu Stable Release Updates, which is updated by the same job that does the phasing. At the time of publishing this post, the update percentage of the VirtualBox packages stands at 60 percent of users.
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do this sudo apt-get install aptitude -y
sudo aptitude safe-upgrade
see if that fixes it sorry for late reply