Programmatic merge of MP4 Flip videos via CLI

We need someone to install, compile, configure and deploy the necessary software for joining MP4 files that are generated by the popular series of Flip brand cameras. We have an opening bumper video and a closing bumper video, both of which are m4v files that were generated via Flash. These work fine and we are able to join them using a variety of tools, such as MP4Box and mencoder. However, the Flip video needs to get sandwiched in between these 2 bumper videos and it's something that needs to happen via CLI, since it's going to occur immediately after a user uploads their Flip video to the server. We will provide the opening and closing bumper videos as well as Flip cam footage to test with. Ideally we would use GPAC/MP4Box to achieve this task, but we are open to suggestions since MP4Box deems that the Flip cam video files are "not valid IsoMedia files". The final merged videos will need to be playable via HTML5 utilizing the popular jPlayer. We can have this all set up for you to test on--so you will not need to create the or configure a player. All you need to do is get a script working that generates valid merged mp4 files for us to stream. Whatever solution is used, it will need to be deployed on two servers - first our staging environment and then our production environment. Time is of the essence with this request. We are thinking this should be a rather straight-forward task for someone experienced with the configuration and compilation of the various codec libraries.