The user must authenticate twice to access the application SSO/APM

Where are they authenticating twice? Once in APM, once in application? What is the application? What is the SSO method(NTLM, Forms, Kerberos, etc)? Is this a portal resource? Where is the SSO method assigned, on the Access Policy or within resource items of a portal resource?

Your request has left more questions than answers. Perhaps providing more information will get you to an answer faster.