Gary, since you've got the plugin installed on a clone (so you're the only customer accessing that "clone"), you could create me a debug-file and send it to me via PM.
It's important to note at which point the shipping doesn't get included in the total. Is it the very first time you "hit" the checkout_one page after you've logged in? I'm "assuming so", so:
- Log off of the store front.
- Log into your admin and set the One Page Checkout Settings, Debug to true.
- Sign back into your storefront, place a product in your cart and click the Checkout button.
Does the symptom display itself at this point (i.e. no shipping selected)? If so, look in your store's /logs folder for a file named myDebug-one_page_checkout-xxx.log (the xxx is your customer_id), make a copy and PM that to me.
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