Credit note not appearing in VAT return

I'm an accountant. A new client of mine has posted a credit note dated 31 Oct 14 with VAT status "Goods or Services to UK Customer" and 20% VAT. But it's not showing up in the VAT return for quarter ending 31 october 14.

Why this matters to me big time is that 2 years ago this client went on Clearbooks and happily ran the VAT returns with the historic items box not ticked. This in my view is a system weakness - the default should be to pick up all transactions.

Anyway, in my view best practice is to always run this report with this box checked. But in order to do that I need to post a one-off credit note so that the VAT payment ends up right, given that 2 years ago the business paid different amounts to the Clearbooks VAT reports as they knew they were wrong but did not know what was wrong.

Like the other credit note, though, my one-off one is not showing up in the VAT report.