On the summary page there is a Tax Payable section. If there is any tax in your accounts then the amount shows here.
For Flat Rate Tax Scheme I charge 20% and pay HMRC 13%. Therefore the Tax Payable calculation should be 13% of the amount to be charged, before VAT is added. This is what I pay to HMRC. So in my example of £100 billed I add and collect £20 in VAT and pay HMRC £13.
The programme is calculating the Tax Payable as 13% of the amount to be charged INCLUDING 20% VAT. This is clearly more.
Unless of course I have completely misunderstood.