I am using a script to transcode videos to the PS3 like this:

gst-launch-0.10 -v \
    filesrc location="$1".avi ! decodebin2 name=dec \
    filesrc location="$1".srt ! subparse ! txt. \
    mpegtsmux name=mux ! filesink location="$1".mpg \
    dec. ! queue ! audioconvert ! audiorate ! audioresample ! \
           audio/x-raw-int, channels=\(int\)2 ! \
           faac bitrate=128000 profile=LC ! mux. \
    de. ! queue ! \
           textoverlay name=txt font-desc="Droid Sans 30" ! \
           x264enc pass=cbr bitrate=1024 me=umh subme=6 ref=2 threads=0 ! \
           queue ! progressreport ! mux.

Using this with some files which have ac3 audio makes them sound with "clicks". The problem is solved if I remove the audiorate element.