Sorry to take so long replying. I just saw your message
Yes, the QuickBooks customer services team helped me to get it straight. It turned out the problem arose on our last VAT filing. We filed a day early and that put the next one out. Quickbooks thought we should file a return for the one day that was missing from the month.
The fix was to get the support team to unfile the last filing so that I could refile it in QuickBooks with the corrrect end date. All is good now.