In case anyone else stumbles across this thread I would like to say how amazing Angelleye's support has been for me and this issue. Immediate response, and we seem to have fixed the issue.
The issue was a mixture of:
• An outdated cart_total.php file (I updated)
• A possible issue with PayPal PayFlow in Woocommerce. Angelleye logged in to the site, looked around at the various settings to make sure it seemed ok and resaved them all. It seems that some people had problems solved by simply resaving, so I guess certain data was stored in depricated table names or blanked during one of a million updates of the million or so components
Thanks again. Hopefully that will be that!