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 it to your transactions. You can run a return for a single period up until the point where you update the VAT return, which makes it easy to compare against 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 transactions on the return against those in your nominal account identifies any discrepancies. Correct these by reversing and re-entering the relevant transactions, or by using the Corrections module.