I had the same problem but with a xfs and a reiserfs partition. I think the problem is that mountall parses /proc/filesystem for the supported file systems but some file systems are implemented as modules (see bug #433672). I have modified /etc/mkinitramfs/modules with the entries for my file systems and updated initramfs with "sudo update-initramfs -k all -u" and now my system boots again.
I had the same problem but with a xfs and a reiserfs partition. I think the problem is that mountall parses /proc/filesystem for the supported file systems but some file systems are implemented as modules (see bug #433672). I have modified /etc/mkinitramf s/modules with the entries for my file systems and updated initramfs with "sudo update-initramfs -k all -u" and now my system boots again.