This is a post from the Numinix forum, and I am having this issue as well. Just wondering if anyone else had this problem, and if so, how you fixed it?

I noticed that when an item that is marked as "always free shipping" the one page checkout (and likely when one page is disabled) shows all of the shipping methods still. I also noticed that no radio button for shipping method is checked. The total calculates correctly, but the other options can be selected still. If you select another method, it reflects the change in the OT as far as pricing goes, but it still says "free shipping" to the left of the updated charge in OT.

I thought this was just an error with my website, but I just test a free shipping product on the FEC demo shop, and the same is true there, the only exception being the other available method is store pickup which also has $0.00 price.

It looks like in the js on the checkout/header_php.php and in the tpl_checkout_stacked.php files it looks for whether the cart has only "always free shipping" items, but doesn't appear disable/not show the other methods like it should (imho).

Any thoughts?
Thanks!