To best assist you, may I ask a couple of questions to narrow this down for you?
Was the payment linked to the invoice when you recorded it?
Did the customer pay via email using Merchant Services?
If you manually recorded this payment and it was linked to the invoice, I suggest clearing the cache from your browser. Web browsers collect cache (cookies) to save you time when loading repetitive data and images, which can cause similar issues such as missing payments. Below I've included the steps on how to clear the cache (depending on your browser):