I have been using this script quite successfully. The results are perfect because it is using raw video.
http://trac.ffmpeg.org/wiki/How%20to%20concatenate%20%28join,%20merge%29%20media%20files
Make sure you edit the EXTRA OPTIONS string.
#!/bin/bash
################################################################################
#
# Script name: MultiMedia Concat Script (mmcat)
# Author: burek (burek021@gmail.com)
# License: GNU/GPL, see http://www.gnu.org/copyleft/gpl.html
# Date: 2012-07-14
#
# This script concatenates (joins, merges) several audio/video inputs into one
# final output (just like as if all the inputs were played in a playlist, one
# after another).
#
# All input files must have at least one audio and at least one video stream.
# If not, you can easily add audio silence, using FFmpeg. Just search the
# internet for "ffmpeg add silence".
#
# The script makes use of FFmpeg tool (www.ffmpeg.org) and is free for use under
# the GPL license. The inspiration for this script came from this FAQ item:
# http://ffmpeg.org/faq.html#How-can-I-join-video-files_003f
#
# If you find any bugs, please send me an e-mail so I can fix it.
#
################################################################################
#
# General syntax: mmcat ...