Post indexer, how to fire auto cron?

I am using post indexer for a rather large wpmu-setup +300 blogs. The indexer works fine when firing the cron manually. Is there a way to have the site auto-index every 5 minutes?
I cannot get new posts to show..

Also when listing blog posts after indexing. Comment count shows 0.

I have a custom function found in this forum with the following code
<?php echo get_comments_number($postid); ?>
but it shows 0 after index.

Any clues here?