What version of IS and fix level you have? In the past, there were some issues reported related to Login has timed out. Below is the readme fragment.
When an Integration Server contains a large number of triggers for process
engine, Integration Server writes a “Login has timed out” error during start
up and shut down.
When Integration Server contains a large number of webMethods messaging triggers
for process engine and Universal Messaging is the messaging provider, the
Universal Messaging client code on Integration Server sends signals to terminate
the thread that is attempting to acquire a connection to the database. This
resulted in errors like the following during start up and shut down:
java.sql.SQLException: [SoftwareAG][Oracle JDBC Driver]Login has timed out.
This issue has been resolved by modifying the way in which Integration Server
interacts with the thread management code in the Universal Messaging client.