Ok I figured this out and the bug was actually reiserfs. Please close
this bug as invalid.

How I fixed it:
- booted into runlevel 1
- rsync -ap /var/ /tmp/reiserfs-sucks
- unmounted /var
- mkfs -t ext3 /dev/sda7 # /var partition
- sudo sed -i '/var/s/reiserfs/ext3/' /etc/fstab
- sudo mount /var
- rsync -ap /tmp/reiserfs-sucks/ /var
- reboot

Strangely enough, dmesg showed 0 errors so reiserfs was doing something
funny. As root, I was unable to even ls -l any of those files. I guess
reiser3 isn't much better off that the out of tree reiser4.

Moral of the story: Friends don't let friends use reiserfs

-- 
package m4 None [modified: /var/lib/dpkg/info/m4.list] failed to 
install/upgrade: unable to open files list file for package `xsane': Permission 
denied
https://bugs.launchpad.net/bugs/288467
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