We have determined the root of the issue is that the certificate used was issued to the Windchill servers real name in windows, and the DNS name that the users are using to connect was listed as a subject alternative name, PTC tells us it MUST be issued to the DNS name that the users are connecting to, as JAVA is not associating the certificate with the url (even though it is listed in the SAN attribute field!). We are generating a new cert, hopefully that fixes us up. Thanks for pointing me in the right direction Binesh
~Ian