Actually, the physical smart card is not being used in this test, the cert from the card is loaded into the client Browser. When it runs, it asks if if the loaded cert is th correct one, and you click yes and it continues.
I've tried debugging the app on the ESXi server. I know the cookie that is suppose to contain the username from the cert is blank, but I can't figure out why. I can also take the now broken version of the VM and run the converter again and pull it back to my PC and run it on workstation, and it works....