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PowerPoint (and the Viewer in this case) does nothing to control timing. It plays your slides according to the timings that you set, but movies and sounds are just "played" at the rate possible, given the resources available.
When you put a presentation on a CD it is now playing from the CD drive (slower) rather than the hard drive (faster). CD drives will probably always be slower than hard drives unless they revolutionize the technology.
Sometimes this means that you have to have two versions of your presentation (one for HDD and one for CD), if you can't or don't want to change the design. If a sound plays for only one slide, the timing issue is less noticeable. However, when you are playing a sound file over multiple slides, the best you can do is reduce the number of slides it needs to synch with.
To make matters much worse, all CD drives are different, in terms of speed. There is no science to this. Some people merge their sound files into a single one and loop it, so the only break point is on the last slide of the presentation. Others break their sound files into smaller ones. Still others eliminate sound all together. I tend to use sound only as a mood
I know that doesn't help, but I do hope it explains what is going on and gives you some ideas.