Had the same issue. Found the reason, it was because I untar-ed the rootfs in a windows machine and copied it to the host linux machine, so some symbolic links were lost.
I have a very similar issue after mistakenly installing PAE on a 64-bit Ubuntu 14.04 machine. Currently it seems to make sense to just reverse the process if that will return the ‘init’ file to the original state before the install. I can only run the machine using a livecd to gain access to the affected drive. How can I process to reverse my install settings?