What version of EI are you using? Are you working from the main computer or the web access?
Double check your payments for the customer to make sure they were applied properly. Is it possible it took $10 of the payments and applied it to another invoice of theirs? EI can be tricky when applying payments, especially when they are applied to invoices that are out of order, as when a customer pays a newer invoice before an older one for some reason.
Did you start before Jan 1 of this year? If so, try running a statement from when you started to see a longer history of credits and debits to their account.
From the main computer, go to the customer profile and click on the INFO tab. This will show you what the current customer balance is. Does this agree with the statement?
Are you sure all of the payments were entered correctly? Did an operator error occur?
Hope this helps!