The rather standard pipeline shown later in this report results in a couple of warnings and report of an internal flow problem. I beleive the cause may be rooted in the mpegtsmuxer, but it me also be in other plugins. Here are the warnings reported:

(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3911:gst_pad_push_data:<mpegtsparse2-0:src> Got data flow before stream-start event
(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3916:gst_pad_push_data:<mpegtsparse2-0:src> Got data flow before segment event
(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3680:gst_pad_chain_data_unchecked:<queue4:sink> Got data flow before stream-start event
(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3685:gst_pad_chain_data_unchecked:<queue4:sink> Got data flow before segment event
(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3911:gst_pad_push_data:<queue4:src> Got data flow before stream-start event
(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3916:gst_pad_push_data:<queue4:src> Got data flow before segment event
(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3680:gst_pad_chain_data_unchecked:<tcpserversink0:sink> Got data flow before stream-start event
(gst-launch-1.0:14875): GStreamer-WARNING **: gstpad.c:3685:gst_pad_chain_data_unchecked:<tcpserversink0:sink> Got data flow before segment event
WARNING: from element /GstPipeline:pipeline0/GstTCPServerSink:tcpserversink0: Internal data flow problem.
Additional debug info:
gstbasesink.c(3264): gst_base_sink_chain_unlocked (): /GstPipeline:pipeline0/GstTCPServerSink:tcpserversink0:
Received buffer without a new-segment. Assuming timestamps start from 0.

The pipeline used is this (gstreamer version 1.1.4)

#!/bin/sh
RAWAUDIO='audio/x-raw, rate=(int)44100, channels=(int)2'
ENCAUDIO='audio/mpeg,mpegversion=4, stream-format=adts'
RAWVIDEO='video/x-raw, width=(int)1280, height=(int)720, framerate=(fraction)25/1, pixel-aspect-ratio=(fraction)1/1'
ENCVIDEO='video/x-h264, alignment=au, stream-format=byte-stream, profile=(string)main'

/usr/local/bin/gst-launch-1.0 -v \
        audiotestsrc is-live=true !\
        queue                   !\
        $RAWAUDIO               !\
        audioconvert            !\
        faac bitrate=128000     !\
        $ENCAUDIO               !\
        queue                   !\
        muxer. videotestsrc is-live=true !\
        $RAWVIDEO               !\
        queue                   !\
        x264enc tune=zerolatency bitrate=2000 !\
        $ENCVIDEO               !\
        h264parse               !\
        queue                   !\
        mpegtsmux name=muxer    !\
        tsparse                 !\
        queue                   !\
        tcpserversink host=0.0.0.0 port=5012 sync-method=2

The issue was first reported here http://lists.freedesktop.org/archives/gstreamer-devel/2013-September/042967.html
and then commented by Tim-Philipp suggesting creating a bug report.