The slideshow timing for QT Movies is independent of the timing for the internal ProSelect slideshow. These are controlled in the Preferences -> Slideshow Tab while the QT movie timing is set in the File -> Export -> QuickTime Slideshow dialog.

When making QT slideshow movies, you have more precise control of this timing so you can exactly match the movie length with your selected music. As such it should be possible to get the QT movie timing close to the same as it was when you ran the slideshow in ProSelect.