Well i looked in the video_conversion.log, and i realized, the converter moves the flv file instead of converting, so i looked into include/functions_upload.php, and realized that this row has to be changed
if ($file_extn == 'flv')
After this change everything is okay. Reason: code was set to move instead of converting when their extension is .flv, which is allright if you just want converts to flv. BUT when you want your flv-s to convert into mp4, then my change has to be implemented, else, the script just moves the file without converting it.
if (($file_extn == 'flv') && ($video_output_format =='flv'))
ps.: i tested it , everything is OKAY NOW.