OK, I've been able to solve this manually.

I had to add a new line in /etc/crypttab for the LUKS encrypted
partition that had my root system. I have another LUKS encrypted
partition for my SWAP and /tmp that was already present in
/etc/crypttab

In my case, to get the UUID

root@pomeron:~# blkid /dev/sda6
/dev/sda6: UUID="b44fed8d-2a58-4d70-ba19-eaf76c5f1b11" TYPE="crypto_LUKS"

root@pomeron:~# nano -w /etc/crypttab
# <target name> <source device>         <key file>      <options>
pomeron UUID=b44fed8d-2a58-4d70-ba19-eaf76c5f1b11 none luks
...

root@pomeron:~# update-initramfs -c -k 3.11.0-19-generic
update-initramfs: Generating /boot/initrd.img-3.11.0-19-generic
/usr/share/initramfs-tools/hooks/intel_microcode: 136: 
/usr/share/initramfs-tools/hooks/intel_microcode: prepend_earlyinitramfs: not 
found
E: intel-microcode: failed to prepend early firmware to initramfs
W: intel-microcode: will try to use late initramfs update mode...

root@pomeron:~# lsinitramfs /boot/initrd.img-3.11.0-19-generic | grep cryptsetup
lib/libcryptsetup.so.4
lib/cryptsetup
lib/cryptsetup/askpass
sbin/cryptsetup


This was NOT needed before and it seems that the only way of solving this is 
manually, which is pretty bad :(

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https://bugs.launchpad.net/bugs/1237556

Title:
  cryptsetup removed from initrd.img on upgrade to 13.10

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