First of all, this is not an issue, is a question.
Can you please point me in the right direction on how to convert a raw h264 stream file to mp4? I tried to follow the test application, but I'm not sure I understand where the raw data will go.

In the test application you have the following code:

    // == Append video data
    for (i = 0; i < 30; i++)
    {
        MP4E__put_sample(mp4, id_video, idr, sizeof(idr), 0, MP4E_SAMPLE_RANDOM_ACCESS);
        MP4E__put_sample(mp4, id_video, frm, sizeof(frm), 0, MP4E_SAMPLE_DEFAULT);
    }

Is the frm constant the array that contains the data for one frame?