Bulk payments

Hi, 

I am having a problem with QB working out the correct VAT. 
i invoice weekly but the company pays a bulk payment at the end of the month. The system doesn't recognise the bulk amount as corresponding with the individual invoices. 
When I work out the VAT I owe, it is a lot lower, almost double, than what it should be? I think this may be because the system is Charging VAT for the individual invoices aswell as the bulk one?