Hello,
Normally agent logging behaviour is controlled by a property log4j.logger.IntroscopeAgent in your agent profile file (IntroscopeAgent.profile) and to prevent console output the string "console" should not be included in that property.
By default the property should be "log4j.logger.IntroscopeAgent=INFO, logfile" which will prevent console output.
The above "Confile search path..." output is not something I am familiar with and it looks to be standard output coming from somewhere else. It also includes Tomcat jar files, so was the "Confile search path..." output definitely not there before you enabled the agent?
Have you just installed the standard OOTB Tomcat agent with no customisation?
Thanks
Lynn