Hello,
1. I’ve checked both products and Shipping information is shown for both:
http://storage3.static.itmages.com/i/15/0507/h_1431019907_1684583_8bd2b2f151.png
Try to clear browser cache and check again.
2. You need edit the files in the directory wp-content/plugins/woocommerce/templates/emails/ and select a file due to order type.
Regards,
Eva Kemp.