Do others charge a fee to customers when an operational stop pay is placed on the system after return of an unauthorized ACH entry ? Wouldn't this seem to be contrary to Regulation E and possible violation for not making the customer whole ? Input is appreciated.

The commentary to 1005.11(c) tells you why this is not an acceptable practice.

3. Charges for error resolution. If a billing error occurred, whether as alleged or in a different amount or manner, the financial institution may not impose a charge related to any aspect of the error-resolution process (including charges for documentation or investigation). Since the Act grants the consumer error-resolution rights, the institution should avoid any chilling effect on the good-faith assertion of errors that might result if charges are assessed when no billing error has occurred.

Thank you for the directive BrianC!