I also have this issue.  I have a bank transcactions that are coming in on the credit card processor.  And yet an invoice and payment has already been processed.  The odd payment is not showing up in the match transaction screen.  This doesn't seem to have anything to do with which account it is being put to (neither undeposited or the actualy bank), it also doesn't have to do with the date range or the amount or it being split entry or not.  Rather it just isn't showing up.  QB desktop cleanly shows all payments in the deposit screen.  But QBO seems to have a glitch.   Please advise.