I found a problem with Ampache when retrieving the track numbers for m4a files. I found a quick hack here that can fix this problem, and allow Ampache to get the actual track number for each song, rather than saying that every song has a track number of 0. http://ampache.org/forums/viewtopic.php?f=2&t=1348

For those who just want the code, you have to edit {ampachewebdir}/lib/class/vainfo.php. Open this file, and find the get_info() function, and paste this at the bottom above the line unset($this->_raw);.

if($this->tags['quicktime']['track']==0) {
    $this->tags['quicktime']['track']=exec('faad -i '.escapeshellarg($this->filename).' 2>&1 |grep track: |cut "-d " -f2',$retval);