An alternative to oscarplu's suggestion:

If you have a movie that has desync'd audio/video, first have a look at the two rows in timeline mode (video and audio): They should be the same length. Zoom way in if necessary to the end of the movie. For some reason, even though video/audio tracks are supposed to be grouped by default, they become ungrouped so that if you delete a video object, the audio object remains, throwing the audio off.

Try this:
-File/Manage Movies/Remove Movie
-Go to Edit mode and select the raw video files (using control-left click) and add them to the time line by dragging.
-MEP15 will still remember the scene information
-If the movie is made up of more than 1 video file (It will if the video is more than 4GB long), select each 'section' at a time (make sure that the audio is also selected automatically: If it isn't, multi-select them both and select Edit/Group) and then Effects\Video Object Effects\Scene Recognition.
-The scenes should aleady be there from before. If not, click "start search" and wait.
-Select the options you want and click "ok".
-Do the same for the other sections of your movie (if necessary).

For me, this works perfectly. I personally appreciate the automatic audio drift detection and have found it to be invaluable. However, within the program itself, something happens LATER in the workflow that ungroups and/or desyncs the video/audio streams.

Hope this helps!
Russell