The Cypress USB-Serial Configuration Utility version I am using is 220.127.116.11.
This problem has been resolved. When the part is setup in self powered mode the VCCD pin and VDDD pins need to be shorted together. This is stated in table 2 of the data sheet but the schematic in Figure 4 on page 17 does not show this connection. If there are any Cypress people who are reading this please update your documentation so no one else runs into the same problem I had.