This issue is really causing my head to spin. I had been using Jenkins to do our maven build for a java project. I'm using FitNesse as the acceptance test framework. When I point FitNesse to the classes generated by Jenkins everything works as expected. However, if I do a maven build with TeamCity and point FitNesse to those classes it appears that the log4j.properties isn't being used. This is a problem because the logging within FitNesse is showing debug messages for all third party jars which spits out way too many lines to stdout. The frustrating part is that I compared the output from Jenkins to that of TeamCity and they appear to be identical.
I really don't know why this is happening, it makes no logical sense. All I do know is that I eliminated as many variables as I could and the only thing that appears different is TeamCity generated build output versus Jenkins build output. This is why I came here in some hope that this makes sense to someone.