Because samba-server is configured with --with-piddir=/var/run/samba, it tries to use that directory for its pid files, and fails as that directory does not exist (by default). Even if that directory is created, the init scripts fail to stop smbd because they expect the pid file to be created in /var/run. I would suggest passing --with-piddir=/var/run, so all the pid files are created in the same directory as most of the other pid files.
and the implication is that `/etc/init.d/samba start` no longer works -- it just silently fails (well, it is logged via syslog, but that isnt friendly)
*** Bug 284629 has been marked as a duplicate of this bug. ***
Fixed by flameeyes, thanks for the bug report.