Creating symlinks from /etc/init.d/samba.{smbd,nmbd,winbind} to /etc/init.d/samba as suggested in the messages from the samba ebuild does not work without also making /etc/conf.d/samba.{smbd,nmbd,winbind} symlinks. Perhaps the init script could be made so it loads the proper config file, or the ebuild messages could be changed to indicate that the conf.d symlinks are also necessary.
Other bug has more info for the same issue. *** This bug has been marked as a duplicate of bug 286738 ***