I had this problem and it turned out it was Apache's permission on the public directory.
Note: I am running Ubuntu 14 on AWS
After installing FFmpeg I had to change the /var/www/* ownership to www-data.
sudo chown -R www-data:root /var/www
(the www-data is the important part here)
Then I had the following code running, and it works when I access it via URL (Apache)
// test.php
$run = system("/opt/ffmpeg/bin/ffmpeg -i /var/www/html/input.mp4 -vf scale=640:480 /var/www/html/output.mp4 &");
if($run) {
echo "success";
} else {
echo "failed";
}
The /opt/ffmpeg/bin/ffmpeg is where my FFmpeg is running from. Yours might be /usr/bin/ffmpeg or something else. You can locate it by typing locate ffmpeg in the command line and looking through the list it gives you.
The input file was a public .mp4 file and the output.mp4 file was going to the same location.
Run this in your command line: php test.php - works
Run this from your browser: yourwebsite.com/test.php - works