Did you remember to change the tracks to Dual Mono?
Also, you can do this the long way:
1. Export each track as its own audio-only QuickTime movie/AIFF.
2. Open the video movie file in QuickTime Player.
3. Open each audio file, APPLE-A, APPLE-C (Select All, Copy).
4. Select the video movie file, make sure the playhead is at the beginning, OPTION-APPLE-V (Add to Movie). Repeat for each audio track.
5. Now do a Save As on the video movie file with a different name, self-contained. This will create a split-discreet-track QuickTime movie.
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