In Kenya, you don't get your VAT refunded, our revenue authority rather starves your cashflow. They say you will recover thru your future sales. This means that, upon filing, your negative balance should remain. It looks like QB assumes that businesses get refunds as after filing that negative balance is nowhere to be found... how do I adjust my sales tax account to reflect the correct figure?
You could do a journal or adjust the VAT. However if you are using the UK version of the software its set up for a refund to happen so we wouldn't be able to advise on what you should do and you would need to speak to a trained and qualified accountant who would be able to help you find out how to work around this.