If you have a difference between your VAT return and your VAT nominal account, there are a number of things you can do to reconcile this and find the difference you are seeing:
Check for any transactions in the VAT control account that are of the type JNL (journal) as these will not be included on the VAT return
Check for any transactions that have used a VAT code of 0 but have a VAT value - if this is the case, the VAT will not be included on the return.
Use the detailed VAT return report and compare this to the transactions themselves - remember that up until the point where you update the VAT return - you can do a return for a single period so this can be compared to the same transaction period on your nominal account.
Remember that if you use multiple VAT accounts you must take all of them into account when comparing your figures.
Comparing the transactions included on the return against the transactions showing in your nominal account should allow you to locate any issues coming from transactions so that you can correct these either by reversing and re-entering the relevant transactions, or by using corrections module.