If you are finding that the information in your VAT Return boxes are incorrect, then you will need to check that your VAT Codes are set up as you expect. To do this:
Click System, VAT, VAT Rates
Select a VAT Code.
Look in the VAT Return section. This will tell you what boxes this code updates and for what transactions.
This can also be caused by certain types of transactions for example Bad debt transactions. They will appear in the output columns, but will not update Box 1 but rather Box 4, as per the HMRC guidance, "Relief from VAT on bad debts" (VAT Notice 700/18).