[Plugin: WooCommerce] Shipping amount on order not given to Paypal

I am using the WooCommerce & WooCommerce Table Rate Shipping plugins with no previous problems. Last night an order went through, on the website invoice generated by WooCommerce, the shipping is shown correctly as $5.70. However the order was put “on hold” because the amount paid by Paypal was not the same. When I opened the Paypal transaction, the website generated shipping amount was shown as $0.00, making the paypal total $5.70 less than the website order total.

I have contacted Paypal about it and they said it was nothing done by Paypal, that somehow the website sent the order through to Paypal without the shipping amount. We have tried replicated the issue by putting through additional “fake” orders but the shipping seems to go through fine.

We have not altered any settings. The only thing to note is that WordPress told us to update our version this morning, which we did, but this was after the order went through last night. The plugins are all up to date.

I don’t know where else to check or where to go from here to prevent this from happening again. Any suggestions?