There are various reasons that there could be a difference, check for the below:
Double check in the nominal that there haven't been any other Journal postings other than the journal to the VAT Payable account, these journals don't affect the VAT return so postings should be corrected not journaled.
Check all the VAT Payable journals are correct for the payments made to HMRC each quarter, look at when the nominal balance started to not equal zero after the journals were done to the payable.
Once the difference amount is known export the nominal ledger for the nominal needed and the VAT return sent in that quarter and manually check which ones have been submitted.
