Sam,
What's happening is PowerPoint is no letting go of the screen. If you play a video that also has audio after a PowerPoint cue, you will actually hear the audio which means the video is playing, but PowerPoint has not released the screen. We commonly see this with the newer versions of Office and why it works correctly in V6 is puzzling. The only thing that I can think of is, in V6 you may have used the "Import" option which converts the slides into images and creates a multi-page Media Cue. To test, simply open one of the scripts you created in V5 in V6 to see if you get the same behavior.