Hi. Are you indexing http://www.nexen.net/docs/php/annotee/indexes.functions.php at level one? If not already done, perhaps try to be selective when indexing a site by choosing the most relevant page to index at level one. Also, if available, perhaps try to index from shell rather than with the browser interface. If indexing from shell, the following can be set in the config file to limit the level to one.
PHP Code:
define('SPIDER_MAX_LIMIT',1); //max recurse levels in sipder
define('SPIDER_DEFAULT_LIMIT',1); //default value
define('RESPIDER_LIMIT',1); //recurse limit for update