After saving a movie the background music timing goes out, ruining my video

I made a video and the background music is important as I have matched up little things to the high points in the music.

However when I save the project the video files go a little bit out of sync and run on too long, longer than I cut the videos to. This means that when I watch the movie the points in the music are not matched up and it ruins the feeling of the video.

I read that this might be a problem with using mp4 files but I can't very well change everything to a wmv file and then go and spend another 3 hours editing this video. Is there something wrong with your program that you can fix? Please help!