Why do I have a minus amount in vat control account ? I am not VAT registered and my account is not set up for VAT

Hello Stuarthy, 

Welcome to the Community page, 

So the VAT Control account is the amount due on the next tax bill. it will be a minus if you have used a VAT code on an expense to record re-claimable VAT and a VAT refund on your next period. 

You would have had to turn on VAT at some point for this to have had happened. if you go to chart of accounts> click on account history on the control account it should tell you when the VAT codes were used and what transaction has this code on.