Hi there,
Welcome back to the Community. Making sure you're recording your transactions the right way is a good exercise for preventing errors in your books.
It's important I'm able to see what you're seeing on your end so I can better assist you. You're more than welcome to contact our support team using this link. One of our agents will be happy to take a closer look at your account and figure out why QB isn't recognizing the payment.
Otherwise, I recommend contacting an accounting professional to get more info on this. If you're not in contact with one, I encourage you to search for one on our website using this link here. Doing this will help prevent any future discrepancies. Let me know if you have other questions. I'm here to help.