This is due to a bug.
There are working patches for long time stable distros like Debian - for some kernels (not all).
Bleeding edge Distros like Arch, Fedora and Manjaro (fixed) will still have slight problems here.
It can be fixed there too with a Live CD.
And here is the recipe:
- You need to boot with a working live-cd
unlock your encrypted root partition
mount your root partition
chroot into your root partition
update your system to get the fixed cryptsetup package
run cryptsetup close root (as described in the second step)
reboot without live-cd
This might be related to my small cryptkeeper problem
Kernel 4.4 is not affected by this issue.