I have metup with my accountant. We have determined that Manager is doing what it is supposed to be doing in that when I create a Journal Entry it updates the VAT Calculation Worksheet and the Tax Payable Account on the Summary Page which is as intended.
What happened is that I paid the VAT before we calculated the VAT for the Business Mileage and I just needed to do an adjustment on HMRC Website to get the figures to balance as the VAT Calculation Worksheet shows only the incoming and outgoing for that quarter not what is outstanding with HMRC. So as intended.
We think that Manager had a bug a couple of years ago which has since been fixed as this is the only explanation for why there are differences between 2016 and 2017 years.
I have been given the calculations for my Vat on Business Mileage and apparently you don’t claim the full amount as VAT - you are only claiming the petrol amount, not the wear and tear and depreciation etc. This is why the figure for VAT does not seem to correlate to the Business Mileage used.
I am going to use the Calculations to work out the VAT each Business Quarter and that will help to keep things on track.
As such I am closing this question as there does not appear to be any bug anymore as it was obviously fixed and all is now balancing correctly.