Looking at it again I think it's another issue:
If there is more than one type of item in the cart it goes wrong by multiplying base rates by the number of item types. EG:
10 x item A weighs 4.5kg (£1007.50) and 10 x item B weighs 1.5kg (£1,032.50). That's a total parcel weight of 6kg (under the base weight of 10kg) so the shipping should be 13% of total value (0.13 x £2040 = £265.20) + one base shipping charge of £6.75 = £271.95
But it's making it £278.70 (£6.75 too much)
In this scenario it's adding two base shipping charges (as there are two items types).