There are a few things you can check to see what the difference relates to; the VAT ledger Report runs by VAT quarter and shows what is posted to that VAT quarter.
If you check the below areas:
Load up the Nominal Enquiry on the Enquiries tab and find the VAT input and VAT Output nominals check the values for the three months in the quarter.
Also check the value you are out, by sorting in amount order in the nominal this might be one posting that is in the wrong VAT quarter and needs to be changed.
If that doesn't show you the difference and it is more than one transaction, you will need to compare the transactions on the VAT Ledger Report against the VAT Return Report to locate the transactions.