I am guessing that your Add On shipping module is not using the code to manage this feature ...

If you look at one of the core shipping modules, such as Flat Rate flat you will see how the $this->enabled is controlled ...

Example:
Code:
      // disable only when entire cart is free shipping
      if (zen_get_shipping_enabled($this->code)) {
        $this->enabled = ((MODULE_SHIPPING_FLAT_STATUS == 'True') ? true : false);
      }
If you were to add that IF around the $this->enabled for your shipping module then it would work ...

Keep in mind, some do like to pick an alternative to Free Shipping as they are in a hurry ...