run-init: nuking initramfs contents: directory not empty, then kernel panic

run-init: nuking initramfs contents: directory not empty, then kernel panic

I did an apt-get upgrade on my clusters's head node (13.04 server) and
since then it won't boot at all. The system kernel panics very early in
boot with the message: run-init: nuking initramfs contents: directory not
empty. According to the logs, the only packages that were updated are:
python3, libplymouth2, whoopsie, plymouth-theme-ubuntu-text, and plymouth.
I have no idea what the problem could be. Any help is appreciated.