I found the same issue a couple of months ago and thought it was connected to the WooCommerce Product Bundles plugin. However, the support for that plugin did a lot of checking and stated…
“it is possible that the sum of all the individual order items is not equal to the total order price, regardless of the order items product type. The reason why this happens is that WooCommerce core uses different methods to calculate the total order price than to display item subtotals — the former are more extensive and calculate totals with better accuracy”
I tested buying the same products but not via a product bundle and got the same issue so I know it’s not that plugin.
It appears that this plugin uses the Woocommerce subtotals which is where the issue lies. If you check the order confirmation page that appears after a customer has made an order you will see the same issue with the figures on that page. This plugin just reproduces those figures I believe.
A simple solution for this plugin would be to take the actual Woocommerce total and then reduce by the postage cost to get the subtotal – that way all the figures would tie up and from my testing I believe they would be correct (as the actual total is always correct). It’s not ideal as the woocommerce order confirmation page would still be wrong but the long term record is the pdf produced by this plugin: I doubt many customers bother reading the order confirmation page in any detail so hopefully won’t notice. Woocommerce should look to correct it though.
I can supply screen prints if needed,
Terry