There is this guy..
http://askubuntu.com/questions/802468/menu-bar-and-launcher-missing-after-installing-updates-16-04-lts

which addresses virtualbox specifically.

It wouldn't submit, literally nothing happened. Now that was under a
16.04 image that was upgraded to 16.04.1.

When I did a fresh 16.04.1 install into VirtManager, yes, it worked,
right up until I set launcher to autohide, then it was good night
Charlie Brown. . If you are not using an existing 16.04(.0) image then
you can't reproduce the issue. But, as you can see from the above URL,
someone else reported the very same upgrade problem as I did.

SOmething you should take a look at is 1001255, that is likely the
culprit, with the exception of unable to move windows, as I reported as
well as the above url.

Are there no launchpad bugs opened against 16.04.1 re: immovable desktop
windows? Being a VM I am guessing the image's concept of its video
device is done externally like spice/qxl.  Remember, when you first boot
a new image, the launcher is set to autohide=no. Turning autohide=yes
will immediately create the issue. As I mentioned im my comment in the
above askubuntu issue, renaming that subdir simply restores the laucher,
it does not fix autohide=yes.

Ah, very interesting! I brought that image back and the suggested 'fix'
of removing .config/compiz-1 restores the launcher but disables any
effect of setting the autohide. I showed it as autohide on yet the
launcher was visbile. I did restore setting, which turned autohide=off
and then switched it to on and it is showing, regardless of what I do.

I thought I'd try it with a different browser. I see chrome is not an
option so I tried the ubuntu brand browser...it won't let me choose the
file to attach. This stuff, your bug-ubuntu needs some work. This is
crazy. I just tried firefox again and it allows me to choose files but
the Submit Bug Report button is inop.

It appears I can provide no further information. The other thing
Sebastien, if you can not reproduce the bug, you can't verify the fix.

This is a critical bug for me. I can not upgrade existing 14.04 desktops
if doing so breaks them.

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https://bugs.launchpad.net/bugs/1606358

Title:
  Ubuntu 16.04.1 unity disappears when set to autohide

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