vat return problem

I filed the vat on my quickbooks desktop last week as I have done sucessfully for 3 years or so with desktop. Got the report printed and entered the figures onto HMRC site. Paid over the money. When I went to 'pay bills a week or so later the figure to HMRC was there, usually its the same as the return, this time its different by a few hundred pounds, in our favour. When I print the VAT 100 report for the quarter it still shows the figure I paid over to HMRC. Can anyone shed light on what could have caused this? Any ideas to fix?