2nd Audio track from merged .m4v files does not play on iPod Touch

Question

I used Handbrake to encode two .m4v files of a concert DVD that spans two DVDs. I then took those two files and combined them into Quicktime Pro to create a single .m4v file. The file plays fine in QT but when I transfer the file to my ipod, only the first audio track (from the first file) plays. Once the video from the second file plays, the audio is silent. Here's what the movie properties look like:
Enabled Name Start Time Duration Format
====================================================
Y Video Track -- 0:00:00:00 -- 2:21:53:90 -- H.264
Y Audio Track1 -- 0:00:00:00 -- 2:21:53:90 -- AAC
Y Audio Track2 -- 1:27:28:87 -- 0:54:24:02 -- AAC
N Text Track -- 0:00:00:00 -- 2:21:53:90 -- Text
Any suggestions?
Thanks,
Dan

Answer 1

So basically, anytime I combine more than one mp4 file in QT7 Pro, it will always create multiple audio tracks when doing a simple "save as" (vs. export as)
Not exactly. QT has it own set of rules. As you noted, the video track had no problem merging into a single track. This would not have happened if you had merged video compressed differently or added an image/stretched image sequence. Not knowing your specific work flow or settings, I hesitate to make any claims here. Frankly, when merging audio, I normally prefer to use GarageBand when I want to create a single master audio track and still retain control of the other tracks for mixing purposes. However, I could just as well have exported the audio in the original file using QT Pro to a single audio file and used that audio track to replace both original tracks keeping both the original video and chapter tracks. It is all a matter of which work flow you consider easiest for a particular job or project.
If I've exported out my chapter file as a plain text file, how do I go about reintegrating that withing the final mp4 file using QT?
http://www.apple.com/quicktime/tutorials/chaptertracks.html
The above link is a somewhat old tutorial explaining how to create a chapter text track from scratch. Since you already have the chapter track, just refer to the steps indicating how to add the text file back to your main movie file. (Ignore the step that says to set a "Preload" option as this pop-up has been removed.)