I am also experiencing the same issue. Difference being I have a custom JAAS login module, that dynamcially creates user accounts in portal based on data from CAS SSO. Sometimes it takes 30 sec or so to do that which is one of my concerns before deploying.
Since you mentioned you have a custom JAAS login module, thought of asking for help on JBID and JCR tables (though I had asked this in a separate
post and didnt get answer).. I need to know what those tables(JBID_IO, JBID_IO_REL etc) are meant for and what will they hold (basically want to know
interpretations for columns names)