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Hi Carla
It sounds to me like one of the payments (the one that's not showing) has been 'accepted' into QuickBooks by using the 'Deposits' Window perhaps. This needs the Customer name to be entered in the Received From column and the 'accounts receivable' as the account. This tells QBs who the money was received from, so it knows to put the money there - but because it doesn't know anything else about the payment, it doesn't show in the Transactions panel.
The correct way to accept a payment is to go to Receive Payments, either in the Customer Centre, or from the Customers menu, then put the amount, date, undeposited funds or direct to the relevant bank etc. This will then show in the Customer Centre. If an invoice has been raised in advance of the payment, then it should be 'applied' to that invoice that will be showing in the Customer Payment window. If there is more than one invoice showing, make sure the correct invoice is selected.
If the payment is a 'deposit' (i.e. an invoice may not have been raised yet) make sure that no invoices are selected before saving the payment. This way, it gets entered as a credit available. When the invoice is raised, then the payment needs to be 'connected' with the invoice. This is done by going to this Customer Payment screen again, making sure the payment amount is zero, select the invoice that has now been raised and clicking on the Discounts and Credits button, then ticking the relevant payment to make the invoice 'paid'.
Just out of interest - In your settings, (Edit/Preferences/Payments/Company Preferences) have you 'unticked' the Use Undeposited Funds as default deposit account'? This then allows you to have the option of putting deposits direct to a bank account instead of having to use undeposited funds when it may not be necessary.
I hope this may help or give you something to check out.
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