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The drupal ecommerce solution has a problem with the shipping email. On a fresh install of version 3.x the 'shipping notify' option will throw the error message "Mail template for ec_mail_shipping_notification could not be found!". There is this support request on drupal.org that will fix it. Follow the link bellow and apply the patch from JohnAlbin, comment #4. http://drupal.org/node/162512 You should now have a default shipping drop down in the store options.
The drupal ecommerce mode clears the contents of the cart when you enter the payment system. This is annoying because if a user fails the payment there shopping cart is emptied and may have taken a long time to create. I found this one a little hard to debug as it is actually an implementation of hook_ec_transactionapi in the cart itself. To fix this problem just go into the ecommerce module and comment out the line cart_empty in the cart_ec_transactionapi function. You will then need to clear the cart down yourself either in your payment gateway or payment success node.
If you need a London based Drupal developer you can hire me. Check the availability page and contact me on info@aprium.net.