Hi Graham,
I just tried that, it worked for me. In past, I have accidentally entered the amount in "reference number" text-box, in which case, it applies payment to all invoices, because the "Amount" text-box comes pre-filled with total due amount for the customer. You should make sure, applied column shows right amount for right invoice.
If it does not work for you, you may try the official support link posted above by Admin. Any supporting video/screenshots may help.