I have the same problem, I have a couple of short audio files attached to some slides. When the slideshow is viewed in Keynote they are played as they should. However, when exported to QuickTime, some of the audio files are only played until a certain point, with a couple of seconds missing.
I noticed that this started to occur after the "upgrade" to El Capitan. I then tried to export an old file, which I had already exported a couple of months ago and of which I knew that there were no problems with the file, and to my surprise, the new video had the same problems with missing bits of audio.