Upgrading ArcGIS Server .NET from 9.3 to 9.3.1 resets values set within rest.config for the REST Services directory if those values had been configured to reference reverse proxy URLs.
After running the GIS Server Post-Install, reconfigure the values within rest.config to point back to the reverse proxy URLs.*tested to confirm that the Web Apps PI is resetting the .config file (LK) moving to Server area