I am seeing this as well. I'm actually hosting the VM in VMware
workstation 12.5, but the scripts install both VMware and virtualbox
guest tools (so that an OVA is useful in both).

I have an older snapshot that does not have problems, which is using
5.0.40-dfsg-0ubuntu1.16.04.2. The OVA I built today, where X crashes on
startup, got 5.1.34-dfsg-0ubuntu1.16.04.2. From
https://launchpad.net/ubuntu/+source/virtualbox/+publishinghistory, I
don't see any versions between that built for xenial to narrow it down
further.

Uninstalling virtualbox-guest-x11 makes the problem go away; X11 works
again, at least in VMware. Presumably it would now not work in
VirtualBox.

It seems to be happening because virtualbox-guest-x11 is stealing the
alternatives for x86_64-linux-gnu_gl_conf and x86_64-linux-gnu_egl_conf,
even though it's GL libraries won't work *at all* on another host.
5.0.40-dfsg-0ubuntu1.16.04.2 doesn't seem to have alternatives for
these, much less high-priority defaults for them.

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https://bugs.launchpad.net/bugs/1762491

Title:
  No graphics after update, caused by virtualbox

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