The MP4 standard (ISO/IEC 14496-12:2008: Information technology — Coding of audio-visual objects — Part 12:ISO base media file format) envisages that a server will convert an MP4 file to some other format before or in the process of streaming it. It expects the server to have random-access capability to the whole MP4 file. When such a file contains the Media Data Box (mdat) before the file metadata in the
Movie Box (moov) then Squeezeplay's native decoder cannot handle the file. Other streaming envelope formats are available which could be used SbS to resolve this issue.

This issue is discussed at http://multimedia.cx/eggs/improving-qt-faststart (and elsewhere). It appears that qt-faststart will reorder the contents of the file as necessary to make it streamable.