Comment 20 for bug 47768

The problem is in fact with initramfs-tools, but you can work around this problem by using yaird to generate your initrd. Had this problem quite often lately and searched for an alternative. yaird is a quite good one (at least for me ; and I',m using raid + lvm ; bootloader is lilo).

You cannot remove initramfs-tools from ubuntu, so you have to install yaird in addition to initramfs-tools. There are some dependencies wrong IMHO, because with debian you can replace initramfs-tools with yaird.

After installing yaird the only thing you need to do to get kernel packages to generate their initrd with yaird is to add this to kernel-img.conf:

--- snip ---
ramdisk = /usr/sbin/mkinitrd.yaird
--- snap ---

Just reinstall you kernel package and the initrd should be generated correctly.