Getting Agents to work with Custom SSO

[JTesson State University New York Systems]

We'd like to get Agents working but because we use customized SSO we always get errors. Executing an Agent errors because at that point we are already signed in.
We get message like this:
State: 08004. Code: 10018. [NQODBC] [SQL_STATE: 08004] [nQSError: 10018] Access for the requested connection is refused.
[nQSError: 43113] Message returned from OBIS.
[nQSError: 23006] The session variable, NQ_SESSION.SUNY_SSO_USER, has no value definition.
[nQSError: 13011] Query for Initialization Block 'Auth1' has failed. (08004)

It seems to be wanting to run our session initialization block that handles the signin.

Any experiences with this?

Thanks