Hi ejh,
I'm not a developer, but I was able to solve this by editing /administrator/components/com_hikashop/helpers/helper.php around line 2783 there's:
' ORDER BY a.shipping_id, a.shipping_price_ref_id, a.shipping_price_min_quantity';
I just commented that line and placed below:
' ORDER BY a.shipping_fee_value DESC LIMIT 1';
so query is ordering shipping prices of products in cart by shipping fee descending and it's taking only first highest value.
If it's proper way of doing it should tell someone from HS dev team, however as I sad it did the trick for me.
Best regards,
Chris