In case this helps someone, I just upgraded my 16.04.1-64 system to VirtualBox 5.2.
No doubt about it, the VBoxAdditions ISO that comes with it is just plain flakey on my system. They show a fix here. After it flaked on Debian 9 and Ubuntu-MATE 16.04 guests I decided I’m not even going to try the original ISO anymore.
Definitely an improvement. I should listen to my own advice and never use a first release. Hope this helps someone.