OS X :: Unable To Combine Two Video Files With QT Pro?

I have this movie that came in a double-sided DVD. I ripped each side using Handbrake to a .m4v file. Each file plays just fine in QT, iPhone and ATV.

However, when I used QT Pro to combine them to an .mov file, I get the following results:
- QT (and iTunes) plays entire video fine
- no audio from the first half of the combined video when played on ATV
- no audio from the second half when played with VLC

(The instructions I am following are from page 31 of this: [URL])

When I take that combined .mov file and converted to .m4v using Handbrake, I get the following results:
- QT+VLC play no audio on second half
- ATV isn't letting me ffwd and it thinks the entire video file is one big chapter, and I haven't gotten to the second half to know if there is audio (first half has audio)

Now... I know that the issues with the .m4v that I generated from Handbrake doesn't mean much, so let's just focus on my issues with the .mov file if you agree that the .m4v playback issues aren't relevant.

What am I doing wrong with QT Pro when trying to combine the two halves of my movie into one large video file? If it matters, the movie is only 2:27 total length. I've not had a problem ripping DVD movies with Handbrake. And, finally, I can join my two halves on my Windows box using AVS Video Convertor.