If you look at your Accounts Receivable in QuickBooks, is it up-to-date and accurate? Sometimes users will enter an invoice for a customer, then enter a sales receipt when they receive payment, leaving an open invoice in their AR, or they will enter a payment without invoicing the customer first. To find these errors, run a Collections Report. Scroll through this report and make sure everything makes sense: There shouldn't be any negative numbers or balances open on a client that you know you received payment from already.
If you run this report and find these issues, call Jess at 425-401-5061, and she can help you get them cleaned up.