We have also found this occurs, and per Pay VAT tax on shipping charges - #15 by rtimagine @umair states to place the shipping prior to the tax in the charges table and ensuring the tax is set to apply on the previous row total…
Now although that can work, it is problematic given the default tax templates always place the tax first and you add shipping after, so you need to move the items around and also change the tax to apply on the previous row - which is too error prone for end users. We elected to go the single item route for shipping too, however when doing packing slips you need to remember to remove the item as it is a non-stock item and so the packing slip cannot be saved…