Just to add to above. After removing the old version as stefano
mentioned, I did this:

sudo dkms build -m vboxdrv -v 3.0.6 -k 2.6.31-11-generic
sudo dkms install -m vboxdrv -v 3.0.6 -k 2.6.31-11-generic

This rebuilt the module (which was needed for me because of the kernel
upgrade), then installed it. Checking the status shows I've got
everything correct now, and DKMS should setup everything fine on the
reboot.

dkms status
vboxnetadp, 3.0.6, 2.6.31-11-generic, i686: installed 
vboxnetadp, 3.0.6, 2.6.31-10-generic, i686: installed 
vboxnetflt, 3.0.6, 2.6.31-11-generic, i686: installed 
vboxnetflt, 3.0.6, 2.6.31-10-generic, i686: installed 
vboxdrv, 3.0.6, 2.6.31-11-generic, i686: installed 
vboxdrv, 3.0.6, 2.6.31-10-generic, i686: installed

-- 
vboxnetflt: Multiple versions in DKMS. Unsure what to do. Resolve manually.
https://bugs.launchpad.net/bugs/354913
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