Eebygum

I have a problem which is driving me insane. When doing my invoices yesterday, I have come across that many of the customers payments had not registered. So I painstakinglu went through them all again and marked them off as paid. Under the customers list, it shows the invoices that have been paid, and the amounts owing. Only when I go to the unpaid accounts, its showing many of my customers are owing large amounts of money, when they don't. Please can someone advise as to what has happened? I have gone right back through to when I first started using the software in 2012 and still can't get the unpaid accounts bill to show the correct amount.