Let me help you with paying your invoice and VAT in QuickBooks Online.
If the invoice shows that the product you bought is taxable, then select Exclusive of Tax. Thus, you should only pay $1000.
Otherwise, select Inclusive of Tax if the supplier sent you an Ex-VAT invoice. This way, the tax amount will be added to your invoice. Thus, you'll pay $1200.
Please see the attached screenshot for your guidance.
I've added these articles for additional information:
Since you still receive the same error message after following the troubleshooting steps suggested above, I'd recommend contacting our Customer Care Support.
They can pull up you're account, securely, and create a case or ticket ID to be submitted to our engineers for further investigation about this unexpected behavior.
To contact our dedicated support:
Go to Help.
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Enter Error message when receiving payment in the What can we help you with? field.