I am using gstreamer 1.2.1, I found zero timestamps for below mentioned pipelines. Can anybody help me understand this issue. What I understood is best->last_pts and best->last_dts initial values sent to mpegtsmux_collected_buffer function are set to 0, and GST_CLOCK_TIME_IS_VALID infers it as valid time. This is leading to zero timestamps. Am I right here??

The Gstreamer source code I used for testing:
http://gstreamer.freedesktop.org/src/gstreamer/gstreamer-1.2.1.tar.xz
http://gstreamer.freedesktop.org/src/gst-plugins-base/gst-plugins-base-1.2.1.tar.xz
http://gstreamer.freedesktop.org/src/gst-plugins-good/gst-plugins-good-1.2.1.tar.xz
http://gstreamer.freedesktop.org/src/gst-plugins-ugly/gst-plugins-ugly-1.2.1.tar.xz
http://gstreamer.freedesktop.org/src/gst-plugins-bad/gst-plugins-bad-1.2.1.tar.xz
http://gstreamer.freedesktop.org/src/gst-libav/gst-libav-1.2.1.tar.xz

Download the input test file (H264/AAC) from here: http://goo.gl/Vkz0th
Please have a look at Output Logs:
Pipeline1: http://goo.gl/T1vvFT
pipeline2: http://goo.gl/uqBVXt
pipeline3: http://goo.gl/2VoaZe
pipeline4: http://goo.gl/mh8VZo
pipeline5: http://goo.gl/J7pSwP

You can reproduce this issue with below given pipelines.

Pipeline1: Video Audio transcoding. This produces PTS= 0 and DTS=None.
gst-launch-1.0 filesrc location=<file path> ! tee ! queue ! decodebin name=demux ! deinterlace mode=0 fields=1 method=4 tff=0 ! videoconvert ! tee ! queue ! videoscale ! video/x-raw ! x264enc ! mpegtsmux name=mux ! fakesink silent=false -v demux.! tee ! queue ! audioconvert ! audioresample ! volume ! voaacenc ! mux.

pipeline2: Video only transcoding with mpegtsmux. This produces PTS= Valid and DTS= None.
gst-launch-1.0 filesrc location=<file path> ! tee ! queue ! decodebin ! deinterlace mode=0 fields=1 method=4 tff=0 ! videoconvert ! tee ! queue ! videoscale ! video/x-raw ! x264enc ! mpegtsmux ! fakesink silent=false -v

pipeline3: Video only transcoding without mpegtsmux. This produces PTS= Valid and DTS= Valid.
gst-launch-1.0 filesrc location=<file path> ! tee ! queue ! decodebin ! deinterlace mode=0 fields=1 method=4 tff=0 ! videoconvert ! tee ! queue ! videoscale ! video/x-raw ! x264enc ! fakesink silent=false -v

pipeline4: Audio only transcoding with mpegtsmux. This produces PTS= 0 and DTS= None.
gst-launch-1.0 filesrc location=<file path> ! tee ! queue ! decodebin ! audioconvert ! audioresample ! volume ! voaacenc ! mpegtsmux ! fakesink silent=false -v

pipeline5: Audio only transcoding without mpegtsmux. This produces PTS= Valid and DTS= None.
gst-launch-1.0 filesrc location=<file path> ! tee ! queue ! decodebin ! audioconvert ! audioresample ! volume ! voaacenc ! fakesink silent=false -v

I tried with other muxers (like mp4mux, flvmux), where I didn't see this issue.
Please let me know if you require more details.