I can't think of any reason that should happen - have you tried making a new project, copying all the slides into it and publishing it again?
I have had a similar experience going to an AVI file. I had a file that was about 90 slides in length and by the end the visuals ended several seconds before the audio. I broke up the file into 3 parts (30-35 slides each) and it still was a problem - visuals ended before the audio. In troubleshooting one of the parts, I found that the visual on one of the slides was totally skipped - the audio was OK. As a result, the video was out of sync by about slide #20.
The Captivate Preview works perfectly and converting to a Shockwave file works pretty well. However, I've tried converting to AVI using several decoders - all with the same problem in about the same place (~2 minutes into the video). I think it must be a Captivate problem.
I've experienced this type of frustration publishing to SWF format in Captivate 3 which, of course, cannot export to AVI format. I don't know if the solution I've tried will work in Captivate 4, but it's worth a shot.
It was definitely a glitchy thing in Captivate where the program just lost its mind and was ignoring the slides as they were setup. (That's not a professional diagnosis.) In a couple cases, I had to recreate the slide, from scratch, where the issue began and delete its doppelganger. That stopped the issue from starting and the following slides fell in line.
Another time all I had to do was move the audio clips around on the timeline. It was important that I released the clip in a new location before returning it to its original start point. I had to do this on all the affected slides.
There had to be some sort of corruption going on, but these two options helped me at different times. I hope one of them works for you, Robert.