I am experiencing the same problem, with no logging for 8.5.
Initially I experienced the Error "Entry already exist in index" on a unrelated line,
and after some pain I have narrowed it down to the NotesFactory class
If you use OpenLogItem oli = new OpenLogItem() then it uses the NotesFactory class to create the session, we go the error above but there were no agentcontext details in the log.
If you use the following then the logging worked
Session session = getSession();
OpenLogItem oli = new OpenLogItem(session);
This only occurred on classes that extend AgentBase.