Are you on cash or accrual accounting? If it’s cash accounting, you would have accounted for the VAT on this payment at the time the prepayment was recorded rather than on the invoice. Only if the invoice is a different rate to what was specified for the payment would it show in the VAT report.
Are all the client settings set correctly? Is the invoice marked as an EC reverse charge invoice?
If you are on cash accounting the VAT will be accounted for at the time of the payment. Likewise, if you’re on acrual accounting, it will be accounted for on the invoice date.
Regarding the EC sales, please feel free to send me account and invoice details in a private message and we’ll check this out at the earliest opportunity for you.