Need to check that the first line looks like this:

Code:
<?php

$cmd_ffmpeg = "$config[ffmpeg]    etc etc etc
Then comment out one or the other of the next two lines and see which mencoder works for your server. The first one where it says #$cmd....that is "commented out" meaning it's not being used. The second one is what's being used. If you want to try the "old version" to see if that works, put a "#" symbol in front of the second $cmd and erase the # from the first one.

Code:
# For old version of mplayer
# $cmd_mencoder = "$config[mencoder] '$video_src' -o $video_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 -lavfopts i_certify_that_my_video_stream_does_not_use_b_frames";

# For latest version of mplayer
$cmd_mencoder = "$config[mencoder] '$video_src' -o $video_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";