Actually the issue is the transcoding to mpeg. The reason seems that in contrast to upstream, the mpeg2enc plugin and the ffenc_mpeg2video habe the same rank secondary; encodebin seems to select the mpeg2enc plugin then which causes the issue. Moving /usr/lib/gstreamer-0.10/libgstmpeg2enc.so out of the way makes transcoding work again.
Actually the issue is the transcoding to mpeg. The reason seems that in contrast to upstream, the mpeg2enc plugin and the ffenc_mpeg2video habe the same rank secondary; encodebin seems to select the mpeg2enc plugin then which causes the issue. Moving /usr/lib/ gstreamer- 0.10/libgstmpeg 2enc.so out of the way makes transcoding work again.