I am encountering the same issue running IVE6.5R8 and looking to upgrade to 7.0 because we have windows 2008 domain controllers. Did you ever find the solution?
What type of authentication is the site doing? If it is form POST, it should work seamlessly; HOWEVER, if you are using BasicAuth/NTLM/Kerberos, there is additional configuration needed to use these SSO types.
Users>Resource Policies>Web>SSO>General to enable the correct types
Users>Resource Policies>Web>SSO>BasicAuth/NTLM/Kerberos for the resources