I have some similar problems with your plugin (version 2.1.2). In my case totals are right, but coupon discounts and shipping costs decimals are wrongly shown as .00 in order details and mail.
I've notice that order shipping and cart discount are stored in my database with a comma as decimal separator (instead of a dot, as it should be), so I think that's the problem (I'm from Spain, and miles separator in woocommerce is a dot, and decimal separator is comma).
But I don't know why, I've installed a backup in a local server, and it works as supposed with the same config!! (it stores that values using a dot as separator).
Differences between production and local installs are:
PHP:
production: 5.3.29 - local: 5.3.28
MySQL collation:
production: utf8 unicode - local: utf8 general ci