When exporting an MP3 encoded file as Movie, QMidi does not convert the audio stuff unless you altered either the pitch or the speed. SO your MP3 will just be added as is: an mp3 audio track inside the movie file.
... but making a iOS compatible movie from QMidi have some requirements:
Video format: H264
Audio format: AAC (NOT mp3)
You can inspect the tracks format using QuickTime's inspector.
Actually there's no way to skip conversion from MP3 to AAC (this is what iTunes does), you should use AAC from the beginning of your process :-(