So if you type in the command:

Code:
/usr/bin/mencoder '/var/www/vhosts/domain.com/httpdocs/video/video.avi' -o /var/www/vhosts/domain.com/httpdocs/flvideo/1221510242302480554.flv -of lavf -oac mp3lame -lameopts abr:br=56 -ovc lavc -lavcopts vcodec=flv:vbitrate=500:mbd=2:mv0:trell:v4mv:cbp:last_pred=3 -srate 22050 -ofps 24 -vf harddup
Which is from your convert command in an shell, this works? But when your script executes this, it does not? If that is the case, what user are you logged in with when you are executing that command above? Are you logged in as root, or as the user who is the owner of your domain directory?