Look like ffmpeg is not compiled with libx264

Verify following convert command works on the server


/usr/bin/ffmpeg -i '/home/user/public_html/malnarc/video/NEIL-PEART---STROMBO-06-17-2011.mp4' -acodec libfaac -ab 96k -vcodec libx264 -vpre hq -crf 22 -threads 0 -b 500k /home/user/public_html/malnarc/flvideo/4ca4238a0b/13084700571849298773.mp4
If not, you can try using mencoder to convert the video.