PHP System/Exec No Output - No Action - php

Question

I'm trying to convert some videos using ffmpeg into different formats.
I have this class,
<?php
define('FFMPEG', 'C:\\cygwin\\usr\\local\\bin\\ffmpeg.exe');
class VideoEncoder {
public function multicodeFileIntoDir($file, $directory) {
$parts = explode('/', $file);
$filename = $parts[count($parts)-1];
$encode_android = FFMPEG.' -i "'.$file.'" -s 480x320 -vcodec mpeg4 -acodec aac -ac 1 -ar 16000 -r 13 -ab 32000 -aspect 3:2 "'.$directory.$filename.'.g1.mp4"';
$encode_windows = FFMPEG.' -y -i "'.$file.'" "'.$directory.$filename.'.avi"';
$out = shell_exec($encode_android);
$out = shell_exec($encode_windows);
}
}
On debugging the commands that would be run, they work as expected, and produce the correct file. The permissions on the directory I'm calling this code on has permissions as 777, $out is null, and the command has no effect.
I have error_reporting as E_ALL, and display_errors is TRUE.
An example of the command (the value of $encode_windows just before executing) is
C:\cygwin\usr\local\bin\ffmpeg.exe -y -i "C:\xampp\htdocs\cams/../front/vid20110623_122802.mp4" "C:\xampp\htdocs\cams/../front/vid20110623_122802.mp4.avi"
Edit: It seems like it is writing to STDERR, somehow the output of the command is in the apache error log. Still, the output seems ok..
Any ideas?
Thanks