Hi
Check in Storyboard mode that the video is still there. (it should be). You should see the thumbnail of the clip with the duration printed underneath it, but no audio track evident or perhaps just a straight line. If there is an audio track..even a "silent" one VP (AFAIK) will read the MP4 clip as actually having a track. This means that the mp3 will be placed to follow the "silent" audio on Audio Track 1. Until you have added it Audio Track 2 will not be visible.
If the mp3 is a long audio clip relative to the MP4 it will be shown on the timeline full length and the video clip section will have been squashed visually . Zoom in and see if it there at the start.
If this is the case then all you need to do is grab the mpeg3 in Audio Track 1 and drag it down to Audio Track 2 and then along to the left so it plays under the silent video.
BTW. How long is the video clip......?
Nat