@Steve. How are you generating your customer list report? The default reports are here: Reports>>Customers and Receivables>>Customer Contact List and Reports>>Customers and Receivables>>Customer Phone List.
In both reports the Customize Report button is at the upper left. As SkinnyRaven has mentioned, select the Filter tab: active status=yes.
And the filter is set to active only? If so, try toggling the active state of that customer to on. Save it, then go back and in and toggle the active state to off. It isn't a sub-job or anything, correct?