Your video_conversion.php says you are using mencoder

$cmd_all = $cmd_mencoder;

Then how your debug.txt shows ffmpeg ?

Code:
 /usr/local/bin/ffmpeg -i /var/www/vhosts/cubacabin.net/httpdocs/vshar
e/video/Making-Music.avi -acodec libmp3lame -ar 22050 -ab 32 -f flv /var/www/vhosts/cubac
abin.net/httpdocs/vshare/flvideo/Making-Music.flv

The content you posted is the one you use on your server ?