Ah my bad, I have investigated this in RH bugzilla in https://bugzilla.redhat.com/show_bug.cgi?id=961881 before checking if this was filed upstream. I'll c&p my lengthy comments from there.

 Christophe Fergeau 2014-04-07 13:51:33 EDT

I've spent some time on this one. When it's done encoding the file, libflac calls update_metadata() in src/libFLAC/stream_encoder.c which tries to seek at the beginning of the encoded file to rewrite the STREAMINFO header with the computed md5 checksum.
This calls gst_flac_enc_seek_callback() which starts by doing:

    /* try to seek to the beginning of the output */
    query = gst_query_new_seeking (GST_FORMAT_BYTES);
    if (gst_pad_query (peerpad, query)) {
      GstFormat format;

      gst_query_parse_seeking (query, &format, &seekable, NULL, NULL);
      if (format != GST_FORMAT_BYTES)
        seekable = FALSE;
    } else {
      GST_LOG_OBJECT (flacenc, "SEEKING query not handled");
    }
    gst_query_unref (query);

sound-juicer is using giosink, which does not handle SEEKING queries:

static gboolean
gst_gio_base_sink_query (GstBaseSink * bsink, GstQuery * query)
{
  GstGioBaseSink *sink = GST_GIO_BASE_SINK (bsink);
  GstFormat format;

  switch (GST_QUERY_TYPE (query)) {
    case GST_QUERY_POSITION:
      gst_query_parse_position (query, &format, NULL);
      switch (format) {
        case GST_FORMAT_BYTES:
        case GST_FORMAT_DEFAULT:
          gst_query_set_position (query, GST_FORMAT_BYTES, sink->position);
          return TRUE;
        default:
          return FALSE;
      }
    case GST_QUERY_FORMATS:
      gst_query_set_formats (query, 2, GST_FORMAT_DEFAULT, GST_FORMAT_BYTES);
      return TRUE;
    case GST_QUERY_URI:
      if (GST_IS_URI_HANDLER (sink)) {
        gchar *uri;

        uri = gst_uri_handler_get_uri (GST_URI_HANDLER (sink));
        gst_query_set_uri (query, uri);
        g_free (uri);
        return TRUE;
      }
      return FALSE;
    default:
      return GST_BASE_SINK_CLASS (parent_class)->query (bsink, query);
  }
}


Compare with filesink which has in its gst_file_sink_query() method:

    case GST_QUERY_SEEKING:
      gst_query_parse_seeking (query, &format, NULL, NULL, NULL);
      if (format == GST_FORMAT_BYTES || format == GST_FORMAT_DEFAULT) {
        gst_query_set_seeking (query, GST_FORMAT_BYTES, self->seekable, 0, -1);
      } else {
        gst_query_set_seeking (query, format, FALSE, 0, -1);
      }
      res = TRUE;
      break;

However, switching sound-juicer to using filesink is not enough to get the flac signature to be written :( 

gst-launch-1.0 filesrc ! flacparse ! flacdec !  flacenc !filesink does the right thing though, so I guess this is a bug related to flacenc being wrapped inside an encodebin. gst debug log has flacenc 
gstflacenc.c:974:gst_flac_enc_seek_callback: Seek to 26 succeeded
gstflacenc.c:1154:gst_flac_enc_write_callback:<flacenc1> Fixing up headers at pos=26, size=16

but this does not seem to translate to an updated header in the encoded flac file :(

I've been able to reproduce this using (from gstreamer source)
 
gst-plugins-base/tests/examples/encoding -f audio/x-flac -a audio/x-flac  -o /home/teuf/output.flac file:///home/teuf/11k16bitpcm.wav

(wav file came from http://www.nch.com.au/acm/11k16bitpcm.wav linked from https://en.wikipedia.org/wiki/WAV but any random file should do the trick).

After that (metaflac comes with the 'flac' package)
$ metaflac --list --block-number=0 /home/teuf/output.flac
METADATA block #0
  type: 0 (STREAMINFO)
  is last: false
  length: 34
  minimum blocksize: 4608 samples
  maximum blocksize: 4608 samples
  minimum framesize: 0 bytes
  maximum framesize: 0 bytes
  sample_rate: 11025 Hz
  channels: 1
  bits-per-sample: 16
  total samples: 0
  MD5 signature: 00000000000000000000000000000000


If instead I do things manually with:
gst-launch-1.0 filesrc location=/home/teuf/11k16bitpcm.wav ! wavparse !  flacenc ! filesink location=/home/teuf/output.flac


$ metaflac --list --block-number=0 /home/teuf/output.flac
METADATA block #0
  type: 0 (STREAMINFO)
  is last: false
  length: 34
  minimum blocksize: 4608 samples
  maximum blocksize: 4608 samples
  minimum framesize: 214 bytes
  maximum framesize: 7700 bytes
  sample_rate: 11025 Hz
  channels: 1
  bits-per-sample: 16
  total samples: 152267
  MD5 signature: 7ad725dd59f9d1f4bf6d50cf80aee75d

I'll file a gstreamer bug for this tomorrow.

(In reply to Christophe Fergeau from comment #6)
> sound-juicer is using giosink, which does not handle SEEKING queries:
> [...] 
> Compare with filesink which has in its gst_file_sink_query() method:
> [...] 
> However, switching sound-juicer to using filesink is not enough to get the
> flac signature to be written :( 
> 

Rather than hardcoding the output sink, we probably can let gstreamer pick the 'best' one for us through:

 sink = gst_element_make_from_uri (GST_URI_SINK, outputuri, "sink", NULL);

It seems to be picking filesink for local files, and hopefully will use a different sink for non file:// URIs.

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