What shipping modules do you have installed?

What are you using for Free Shipping?

Modules ... Shipping ...
Free Shipping Options freeoptions
-- OR --
FREE SHIPPING! freeshipper

Modules ... Order Totals ...
Shipping ot_shipping

where Free Shipping is enabled for over an amount?

How is Free Shipping indicated?

0 Weight?

Always Free Shipping?

Have you ever touched or customized the:
/includes/classes/shipping.php

We need more details than what you are providing ...