If your VAT specification is wrong check the following:
1) have you created system accounts for VAT Receivable and Payable in your chart of accounts? Read more here.
2) have you posted a transaction directly on your VAT system account without a VAT code? If an amount is shown in your VAT specification on a VAT system account in the 'No VAT code' column then your VAT report will be incorrect.
We do not recommend posting manually to a VAT system account. If you can see that you have done so on your VAT specification, then check the transactions on this VAT system account under General Ledger/Reports/Transactions. Here, the 'VAT' column will be empty (no VAT code shown) when a transaction has been posted manually to this system account.
Read more here.