We've seen a couple other cases like that in the past couple months or so, where the shipping charge is calculated correctly and the transaction details at PayPal's end show the correct shipping amount, yet they failed to include that shipping charge in the final payment amount they processed at checkout.
We've filed trouble tickets with PayPal about those previous cases, so we can file another one about yours; hopefully these reports will help them track down the cause of this bug at their end.
Please email our Support team with the affected Transaction ID, and it would also help if you could attach a screenshot of the Transaction Details from your PayPal account clearly showing at least that Transaction ID, the item price(s) and shipping charge, and the payment total which did not include the shipping charge:
https://www.e-junkie.com/ej/contact.php