I found this discussion because I was having a similar problem. I created a "promotional video" in Keynote. I recorded a narration and music background track in Garageband, which I exported to an .mp3 file. I then selected my soundtrack (.mp3) in Keynote. To get the slides' transitions to sync with the soundtrack, I clicked the "Record" button in Keynote. I clicked the mic mute button right before I clicked the round red "record" button so it wouldn't record any background noise.
When I exported it to "Quicktime", I realized the video was missing the audio. After hours of agonizing over the problem, trying all sorts of things, I contacted Apple support (I still had a few days left of free Apple Care 🙂). The help agents were very friendly and helpful, and they helped me narrow down the issue. I am really excited to have the problem solved!
My problem was muting the mic when I recorded the timing. I guess by muting the mic, I was also muting the soundtrack too. If you want to record the timings without recording background noise (and the clicks of your keyboard buttons 🙂) go to your "System Preferences"-->"Sound"-->"Input" and turn your "Input Volume" (the mic icon) all the way down.
THE KEY IS THIS: DO NOT MUTE YOUR MIC INSIDE KEYNOTE IF YOU WANT AUDIO OUTPUT TO YOUR QUICKTIME VIDEO. This completely solved my problem. Hope it helps you!
If this doesn't help, I highly recommend calling up Apple Support. Click here for contact information. If you have not activated your complementary, free "Apple Care" (might be 30 days-90 days), now's a good time to do that and take advantage of the opportunity to get your problem solved. If you already activated it and it's expired, you can still call them up and talk to an actual person (🙂). They will listen to your problem, and tell you if you need to pay the $29 fee to continue forward towards a solution.