The Invoices on the accounts export are posted as gross which will show the net amount, tax amount and gross amount. What displays in the accounts package should be Gross.

The deliveries and transfers within Advanced Stock Controls are posted as Net. As it should be for stock purposes. When calculating Sales and Stock Values this is always done Net of with VAT.
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The VAT build up would need to be managed outside of Procure Wizard / Advanced Stock Controls, on the accounts package through a journal posting.