Comment 4 for bug 858122

> If you are relying on a one-time script at shutdown to do the migration,
> maybe you need to verify it worked OK and re-run it ASAP in the boot process too.

Unfortunately, the shutdown script itself explains why this is not possible:

        # These must be turned into symlinks for the /run transition. We
        # can't do this at boot time because / is remounted read-write too
        # late, so do it on shutdown instead.

There is no point in the boot sequence when / is writable that we are guaranteed to be able to replace /var/run with a symlink safely, because /run is mounted *before* / is writable and this causes other processes to start up that may be creating sockets in /var/run.

So we really, really need to figure out why this script isn't working for you at shutdown. Unfortunately this is difficult to do since there are certainly no logs from this point in the shutdown sequence, and the problem has not been widely reproducible.

Could you attach a copy of your full /etc/fstab from this system? Maybe something will jump out...