Flat Rate Shipping Errors

Our store’s shipping costs are all out of whack recently. We are using Flat Rate shipping on a per product basis. Shipping is being calculated fine in cart but upon checking out not passed to Paypal (sometimes, sometimes fine). The final price is also showing differently in the sales log view vs. detailed transaction view. The shipping cost is included in log/list view but when clicked does not show shipping in total cost.

There have been some other related issues such as some products passing shipping costs while others do not event though they are configured the same way.

The site worked fine until recent updates.

Any help appreciated. We would even pay an expert to help us.

WP 3.8.1 WPEC 3.8.14.1 (newest)

Thank you!!

https://wordpress.org/plugins/wp-e-commerce/