This pipeline fails:

gst-launch filesrc location=big_buck_bunny_360p24.y4m ! ffdemux_yuv4mpegpipe ! theoraenc ! queue ! matroskamux name=mux ! filesink location=big_buck_bunny_360p24.ogv filesrc location=BigBuckBunny-stereo.flac ! flacdec ! audioconvert ! vorbisenc ! queue ! mux.

This is the log close to the end:

0:00:16.675250492  1042  0x804f070 DEBUG       GST_ELEMENT_PADS gstutils.c:889:gst_element_get_compatible_pad_template: Looking for a suitable pad template in vorbisenc0 out of 2 templates...
0:00:16.675273750  1042  0x804f070 LOG                 GST_CAPS gstutils.c:900:gst_element_get_compatible_pad_template: checking pad template src
0:00:16.675294143  1042  0x804f070 DEBUG               GST_CAPS gstutils.c:905:gst_element_get_compatible_pad_template: compatible direction: found src pad template "src"
0:00:16.675314956  1042  0x804f070 DEBUG               GST_CAPS gstutils.c:908:gst_element_get_compatible_pad_template: intersecting video/mpeg, mpegversion=(int){ 1, 2, 4 }, systemstream=(boolean)false, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-h264, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-divx, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-xvid, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-huffyuv, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-dv, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-h263, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-msmpeg, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; image/jpeg, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ]; video/x-theora; video/x-dirac, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-pn-realvideo, rmversion=(int)[ 1, 4 ], width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-raw-yuv, format=(fourcc){ YUY2, I420, YV12, UYVY, AYUV }, width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ]; video/x-wmv, wmvversion=(int)[ 1, 3 ], width=(int)[ 16, 4096 ], height=(int)[ 16, 4096 ], framerate=(fraction)[ 0/1, 2147483647/1 ];
0:00:16.792762080  1042  0x804f070 DEBUG               GST_CAPS gstutils.c:910:gst_element_get_compatible_pad_template: ..and audio/x-vorbis
0:00:16.792813204  1042  0x804f070 DEBUG               GST_CAPS gstutils.c:916:gst_element_get_compatible_pad_template: caps are not compatible
0:00:16.792827032  1042  0x804f070 LOG                 GST_CAPS gstutils.c:900:gst_element_get_compatible_pad_template: checking pad template sink
0:00:16.792839883  1042  0x804f070 DEBUG       GST_ELEMENT_PADS gstutils.c:930:gst_element_get_compatible_pad_template: No compatible pad template found
0:00:16.792853991  1042  0x804f070 LOG          GST_REFCOUNTING gstobject.c:323:gst_object_unref:<sink> 0x8185a90 unref 1->0
0:00:16.792873058  1042  0x804f070 LOG          GST_REFCOUNTING gstcaps.c:415:gst_caps_unref: 0x80fbfa0 1->0
0:00:16.792907908  1042  0x804f070 LOG                 GST_CAPS gstcaps.c:328:_gst_caps_free: freeing caps 0x80fbfa0
0:00:16.792921388  1042  0x804f070 LOG          GST_REFCOUNTING gstobject.c:442:gst_object_dispose:<sink> dispose
0:00:16.792938778  1042  0x804f070 LOG          GST_REFCOUNTING gstobject.c:474:gst_object_finalize:<sink> finalize
0:00:16.792955121  1042  0x804f070 INFO        GST_ELEMENT_PADS gstutils.c:1209:gst_element_get_compatible_pad:<vorbisenc0> Could not find a compatible pad to link to queue1:sink
0:00:16.792971324  1042  0x804f070 LOG          GST_REFCOUNTING gstobject.c:323:gst_object_unref:<queue1:sink> 0x81833f8 unref 2->1
0:00:16.792985223  1042  0x804f070 DEBUG       GST_ELEMENT_PADS gstutils.c:1768:gst_element_link_pads: we might have request pads on both sides, checking...
0:00:16.793000099  1042  0x804f070 DEBUG       GST_ELEMENT_PADS gstutils.c:1809:gst_element_link_pads: no link possible from vorbisenc0 to queue1
0:00:16.840108534  1042  0x804f070 ERROR           GST_PIPELINE ./grammar.y:614:gst_parse_perform_link: could not link vorbisenc0 to queue1
WARNING: erroneous pipeline: could not link vorbisenc0 to queue1

This one works:

gst-launch filesrc location=BigBuckBunny-stereo.flac ! flacdec ! audioconvert ! vorbisenc ! queue ! mux. filesrc location=big_buck_bunny_360p24.y4m ! ffdemux_yuv4mpegpipe ! theoraenc ! queue ! matroskamux name=mux ! filesink location=big_buck_bunny_360p24.ogv

The only difference is the order of the audio and video pads. matroskamux's audiosink_templ and videosink_templ are both request pads, so I don't really see what could be causing this.