This happens because /opt/var/run is not a tmpfs, and the data is never removed on reboot.
As a workaround, the fs can be mounted as tmpfs on boot before the new Samba is loaded and replaced.
Place the S00runtmpfs file attached to this gist in /opt/etc/init.d, run:
chmod a+x /opt/etc/init.d/S00runtmpfsReboot your NAS. Profit!