It looks like the fix for #1105784 is not applied correctly on upgrades from
broken versions, leaving the users with an empty /etc/modprobe.d/virtualbox-
dkms.conf directory that still generates the warning, in the best case, or with
/etc/modprobe.d/virtualbox-dkms.conf/virtualbox-dkms.modprobe.conf retained but
marked as an obsolete conffile.
The best case probably works like this:
1. preinst renames the config to .dpkg-remove
2. dpkg tries to remove the directory and fails with "Directory not empty"
3. postinst removes .dpkg-remove, the directory stays