I have seen this issue before and it can be resolved by running a reconcile on that customer. You can do this by going to the Sales module then under Utilities clicking on Reconcile. I would run the Current Customer Information one and change the option to print report only then select your customer for the range. Print the report and that will show you what would change by running the reconcile. If you are happy with what you see then you can click reconcile for the option type instead of the print report option.
Let me know if that doesn't work.
Kristen