Latest x264 has an option 'stitchable' which might help with the visual artifacts problem. (helped me with MKV Cutter, with some clips)
About the audio problem, this might be due to different start delays (Hybrid has an option 'fix delay' with delaycut, which might help assuming you reencode the audio).
Other than that I would try to: use mmg to append the files and multiplex to mkv, then remux to mp4 using ffmpeg and then remux the mp4 with mp4box.