Liz,
I just meant when we switched our Windchill installation to Single sign-on we changed the servers to IIS.
From Arbortext when you tried to use PTC Server adapter to connect Arbortext to Windchill it would not validate credentials and return an error.
We needed to have one of our Windchill servers still run Apache as a webserver.
I am also not the server expert but I believe the issue with IIS was that they used NTML authentication. If need be I could try to get more specific details if there were specific questions I could ask our infrastructure team.
Hopefully this helps clarify
Stew