The new Kernel has moved linux/autoconf.h to generated/autoconf.h (hint). I don't really know the technical reasoning for this but anything that includes this in the VirtualBox host module source, needs editing.
Thankfully fixing it is just a case of swapping out the strings:
sudo find /usr/share/virtualbox/src/vboxhost -name '*.h' -exec perl -pi -w -e 's/linux\/autoconf/generated\/autoconf/g;' {} \;
sudo /etc/init.d/vboxdrv setup
Of course this change might not be permanent in the Linux Kernel. Things could go back and that would squiffy your ability to compile in the future so if you need to do the opposite in the future, here it is:
sudo find /usr/share/virtualbox/src/vboxhost -name '*.h' -exec perl -pi -w -e 's/generated\/autoconf/linux\/autoconf/g;' {} \;
sudo /etc/init.d/vboxdrv setup