I came across this post while trying to find a solution to the Free Shipping Qualifier mod not working in my shopping cart due to using the freeoptions module and not the ot_shipping & freeshipper modules. I found a solution that worked for me and wanted to share.
My store version 1.3.9h… in my ot_shipping module I set my free shipping dollar amount to what I wanted and set the Allow Free Shipping to false. I kept my freeoptions settings the way they were. Opened the tpl_shopping_cart_default.php file and found the line that contains
I changed the true to false. Worked fine once that was changed. I do not have the freeshipper module installed.
if (MODULE_ORDER_TOTAL_SHIPPING_FREE_SHIPPING == 'true')