To answer this question you would need to check the Sales Invoice setup in FinOps as each Sales Invoice type can be configured separately and have it's own rules and behaviours related to the VAT, and other fields.
To check the setup you need access to your Hosting.Admin account and the Remote Gateway for FinOps Administrator.
In a Web Browser navigate to the Remote Gateway
Log in with your Hosting.Admin account
Click FinOps Administrator. You may need to enter your Hosting.Admin credentials again
When the application launches log in to the chosen Database.
Click System Options, Sales & Billing, Sales Invoices Setup
From there select the Sales Invoice.
Click Edit.
Note the enabled (ticked) Line Types on the General tab and click the Detail tab
Now change the Line Type selection to the desired Line Type and scroll down until you see the field VAT Code
Check whether this is set to Visible, Enabled, etc.
Also check the Default/Filter setting as this could determine what the value appears as or is set to in the VAT Code field
If you see the words From Stored Procedure in the Default/Filter setting then the setting for the VAT Code will be controlled via a automated SQL Stored Procedure, in the database. If this is the case, please raise a new case online and reference the title of this article and please try to include a demonstration/example of a record which had posted with a different VAT Code/Amount to the Sales Invoice in FinOps.