Wrong use of hook_nodeapi

The submit operation in hook_nodeapi() triggers too early, meaning you don't have access to node id nor node creation date when the node is created. This defeats the purpose of your module.

You should replace your hook_nodeapi() with the following:

function uploadpath_nodeapi(&$node, $op, $a3 = NULL, $a4 = NULL) {
  switch ($op) {
    case 'insert':
    case 'update':
      if (user_access('upload files')) {
          if (isset($node->files)) {
            foreach ($node->files as $key => $file) {
              if (0 === strpos($key, 'upload_')) {  // Only rewrite the name when adding the file, not when updating it
                // Get the new, prefixed file name
            
                $tokenized = token_replace(variable_get('uploadpath_prefix', '') . '/', 'node', $node);
                $tokenized = str_replace(array(' ', "\n", "\t"), '_', $tokenized);
                $dest =  $tokenized . $file->filename;

                // Create the directory if it doesn't exist yet.
                $dirs = explode('/', dirname($dest));
                $directory = file_directory_path();
                while (count($dirs)) {
                  $directory .= '/' . array_shift($dirs);
                  file_check_directory($directory, FILE_CREATE_DIRECTORY);
                }

                // move file on filesystem
                if (file_move($file->filepath, $dest, FILE_EXISTS_REPLACE)) {
                    $node->files[$key] = $file;
                    // update existing file in database
                    db_query("UPDATE {files} SET filepath = '%s' WHERE fid = %d", $file->filepath, $file->fid);
                }
              }
            }
          }
      }
      break;
  }
}

It will just move the file after the file has been saved by the upload module itself which is how it should be done anyway in my opinion.