I have had issues updating Oracle Virtual Box on Ubuntu 16.04.

Sometimes its just doing a manual update after the update and other times it's been crashing after running for days.

IE: many times would run /sbin/vboxconfig after an update and that would fix it until the next update.

Today I utilize Oracle Windows Virtual Box for running Speaker dot exe for my Homeseer 3 lite and Homeseer 3 Pro.

1 - check what Virtual Box versions are installed old and new.

sudo dpkg -l | grep virtualbox

When I ran it I saw three VB's. 4.X, 5.0, 5.1

2 - remove each of the above seen VB's.

sudo dpkg --purge names seen above.

Do this one package at a time.

3 - reinstall Oracle Virtual box clicking on the download link on the Oracle Virtual Box download page and having the Ubuntu software package do the install. This is a bit more plug n play than doing it via command line. Noticed here that the first time I ran it it said that there was an update and provided a link to download it and install it. I did this. Afterwards I downloaded the universal extension pack and installed it using the Ubuntu software package installation utility as before.

Note none of the above deletes the Virtual Boxes you have created. IE: my Homeseer Windows Virtual boxes were not deleted when I did this.