Conflict with WooCommerce plugin?

Hi - I'm having some issues with a conflict between the Australia Post Shipping WooCommerce plugin and BeTheme. I have contacted WooThemes who have investigated and come back with:
"Your Betheme that's currently running is overriding the following WooCommerce templates, meaning they could alter or damage the code and change functionality:"
betheme/woocommerce/archive-product.php
betheme/woocommerce/cart/cart-empty.php
betheme/woocommerce/cart/cart.php
betheme/woocommerce/cart/mini-cart.php
betheme/woocommerce/content-product.php version 1.6.4 is out of date. The core version is 2.4.0
betheme/woocommerce/content-single-product.php
betheme/woocommerce/loop/add-to-cart.php
betheme/woocommerce/loop/loop-end.php
betheme/woocommerce/loop/loop-start.php
betheme/woocommerce/loop/no-products-found.php
betheme/woocommerce/loop/orderby.php
betheme/woocommerce/loop/pagination.php
betheme/woocommerce/loop/price.php
betheme/woocommerce/loop/rating.php
betheme/woocommerce/loop/result-count.php
betheme/woocommerce/loop/sale-flash.php
betheme/woocommerce/notices/error.php
betheme/woocommerce/notices/notice.php
betheme/woocommerce/notices/success.php
betheme/woocommerce/single-product/add-to-cart/external.php
betheme/woocommerce/single-product/meta.php
betheme/woocommerce/single-product/price.php
betheme/woocommerce/single-product/product-attributes.php
betheme/woocommerce/single-product/product-image.php
betheme/woocommerce/single-product/product-thumbnails.php
betheme/woocommerce/single-product/related.php
betheme/woocommerce/single-product/review.php
betheme/woocommerce/single-product/sale-flash.php
betheme/woocommerce/single-product/share.php
betheme/woocommerce/single-product/short-description.php
betheme/woocommerce/single-product/tabs/additional-information.php
betheme/woocommerce/single-product/tabs/description.php
betheme/woocommerce/single-product/tabs/tabs.php version 2.0.0 is out of date. The core version is 2.4.0
betheme/woocommerce/single-product/title.php
betheme/woocommerce/single-product/up-sells.php
betheme/woocommerce/single-product.php

Are you able to offer any advice? The problem is that the Shipping plugin isn't always returning the correct calculations, and we're trying to work out why that might be.

I look forward to hearing from you.
Regards
Melanie

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