It may be that there is either some JD or JC posted to the VAT accounts 2200 or 2201 that wont get picked up on the VAT return.
It may also be that you havent cleared the balances in 2200 or 2201 at the start of the VAT period to account 2202 by either journal or the VAT wizard.
It may be that the VAT figure on the balance sheet includes other accounts other than the VAT accounts?
If neither of these then you will need to run the detailed VAT report and tick it against the sales VAT and purchases VAT nominal for the period to indentify the difference. You will of course need to check that there isnt any opening balances in either nominal at the start of your VAT period as there shouldnt be and check that both figures net to the VAT figure in the balance sheet.
As opposed to actually ticking off you could export the detailed VAT report as a CSV file and sort in excel by size and do the same with the sales VAT and purchases VAT accounts and match them up line by line to identify difference.