Are you sure flash-kernel got called by update-initramfs (it should on
How did you configure u-boot? Maybe you're passing a root parameter
Yeah, I checked all that. After trying *really* hard to figure out how the initramfs hooks for lvm2 and cryptsetup work I ended up chrooting into the rootfs and doing "apt-get purge cryptsetup lvm2 dropbear". That removed all the hooks in /usr/share/initramfs-tools. After that I did update-initramfs -u again and all was ok.