Thumbnails filenames are generated with a question mark at the end : .jpg?

public function run_command($options) {
//    $command = $this->nice . ' ' . $this->params['cmd_path'] . ' ' . $options . '  2>&1';
    $command = $this->nice . ' ' . $options . '  2>&1';
    watchdog('video_ffmpeg', 'Executing command: ' . $command, array(), WATCHDOG_DEBUG);
    ob_start();
    passthru($command, $command_return);
    $output = ob_get_contents();
    ob_end_clean();
    return $output;
  }

  public function generate_thumbnails($video) {
    global $user;
    // Setup our thmbnail path.
    $video_thumb_path = variable_get('video_thumb_path', 'video_thumbs');
    $final_thumb_path = file_directory_path() . '/' . $video_thumb_path . '/' . $video['fid'];

    // Ensure the destination directory exists and is writable.
    $directories = explode('/', $final_thumb_path);
    // Get the file system directory.
    $file_system = file_directory_path();
    foreach ($directories as $directory) {
      $full_path = isset($full_path) ? $full_path . '/' . $directory : $directory;
      // Don't check directories outside the file system path.
      if (strpos($full_path, $file_system) === 0) {
        field_file_check_directory($full_path, FILE_CREATE_DIRECTORY);
      }
    }

    // Total thumbs to generate
    $total_thumbs = variable_get('video_thumbs', 5);
    $videofile = escapeshellarg($video['filepath']);
    //get the playtime from the current transcoder
    $duration = $this->get_playtime($video['filepath']);

    $files = NULL;
    for ($i = 1; $i <= $total_thumbs; $i++) {
      $seek = ($duration / $total_thumbs) * $i - 1;  //adding minus one to prevent seek times equaling the last second of the video
      $filename = "/video-thumb-for-" . $video['fid'] . "-$i.jpg";
      $thumbfile = $final_thumb_path . $filename;
      //skip files already exists, this will save ffmpeg traffic
      if (!is_file($thumbfile)) {
        //setup the command to be passed to the transcoder.
        $options = $this->params['cmd_path'] . ' ' . t($this->params['thumb_command'], array('!videofile' => $videofile, '!seek' => $seek, '!thumbfile' => $thumbfile));
        // Generate the thumbnail from the video.
        $command_output = $this->run_command($options);
        if (!file_exists($thumbfile)) {
          $error_param = array('%file' => $thumbfile, '%cmd' => $options, '%out' => $command_output);
          $error_msg = t("Error generating thumbnail for video: generated file %file does not exist.<br />Command Executed:<br />%cmd<br />Command Output:<br />%out", $error_param);
          // Log the error message.
          watchdog('video_transcoder', $error_msg, array(), WATCHDOG_ERROR);
          continue;
        }
      }
      // Begin building the file object.
      // @TODO : use file_munge_filename()
      $file = new stdClass();
      $file->uid = $user->uid;
      $file->status = FILE_STATUS_TEMPORARY;
      $file->filename = trim($filename);
      $file->filepath = $thumbfile;
      $file->filemime = file_get_mimetype($filename);
      $file->filesize = filesize($thumbfile);
      $file->timestamp = time();
      $files[] = $file;
    }
    return $files;
  }

Here where the actual code to generate Thumbnails using FFMPEG, as far as I can see code is clean and working fine for me.

Can you please reset FFMPEG transcoder settings and try again?