I have had a similar experience with sound and video and believe it is due to the computer nor being able to process the sound and video with any effects such as transitions, colour effects titles, pan / crop events i.e anything that changes the original file needs the computer to work on it. If you try rendering to memory by selecting a small part of your video that experiences the problem and pressing <SHIFT> & <B> theselection will render and then play. If the result is then ok I think you will find that when your video project is rendered out it will then play ok.
I hope this helps
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red.kite Abingdon, England