I don't know what a bad movie atom is, but why don't you try exporting the video before adding the audio (add them together at the end)?
if that still doesn't work, try using a different MPEG-2 decoder (MP2 is different from MPEG-2. MP2 means MPEG-1 layer 2, and is the audio format commonly found in MPEG-1 streams. Likewise, mp3 means MPEG-1 layer 3, and oddly enough mp4 means MPEG-4), encoding to mov with the mp4 codec, then exporting the result to mp4 (file format) in passthrough mode from QTPro, if desired. Some programs that use different MPEG-2 decoders are MacMPEG2Decoder (simplest), MacMPEG2Converter (fastest), and MediaPipe (most powerfull). ffmpeg is probably a fifth option, but you would have to output to divx, not Apple's mp4.