Probably due to a mismatch on TAX CLASSES.
You probably have both "VAT" and "Taxable Goods" as TAX CLASSES in your store.
If you set up your tax class as VAT, then in your product data set define it as "Taxable Goods", it could cause you to have double tax.
If you have EASYPOPULATE installed, use it to download a spreadsheet of your product database. Check the "Tax_Class" column and make sure the word used here is identical to that used in your tax and zone setup.
You can also call up a few products to edit (in the edit console in admin) and see what tax class is applied. If it's "Taxable Goods", choose "VAT" instead, and then do a test checkout with JUST THAT ONE product.
Then, if this is the case, decide on the naming conventions for your tax class, apply the correct factor, then make sure you choose this tax class for appropriate products.
...I am not absolutely sure this is your problem, but I had a similar issue some months ago and this is what was causing it.