mencoder + MP4Box + python script - Fix Audio Issues

Background: We have a python script that is executed as a background process via PHP. The script uses mencoder to merge three videos together into an MP4 video that should be playable via JWPlayer on the Web and via Quicktime / Windows Media Player upon download. The problem: It plays fine on the Web but when you download the video, the audio doesn't play in Quicktime or Windows Media Player. It plays fine in VLC. Our needs: We need two things: 1.) Fix the encoding script so that the resulting videos can be played in Quicktime and Windows Media Player. 2.) Implement normalization on the resulting videos (as it is right now, the intro/outro videos tend to be MUCH louder than the middle video). -- Please read the project first and write the word "Understood". Also write your steps and suggestions to complete the project with a short description of what you understood.