If you have this issue, like we did, it's worth checking that the VAT Refund has been recorded in the correct account, i.e. Bank Account (not Cash, nor PayPal etc.). It's easy to miss the drop-down menu at the top of the Record Refund page.
We were puzzled as to why QB sometimes found a match and sometimes didn't; but when we corrected that, it found the match straight away when we refreshed the Bank Transactions page.
To check, go to:
QB > Taxes > Payments tab > [row for the payment in question] View
Check "Account" shows the correct Bank Account. If not, delete the payment, then redo the Record Refund process, taking care to select the correct account from the drop-down at the top of the page, as well as the other details:
QB > Taxes > Returns tab > [row for the Return in question - Action column] Record Refund
