I just thought of another possibility. Mango 3.x uses Log4J2 where previous versions of Mango used Log4j. If you have a log4j jar that is getting loaded it won't pickup the log42.xml configuration and would probably use some default of only printing to stdout.
I would check your <ma-home>/lib folder and see if there are log4j and log4j2 jars.
ls <ma-home>/lib/*log4j*This should list only these jars:
lib/log4j-api-2.10.0.jar lib/log4j-jcl-2.10.0.jar lib/log4j-core-2.10.0.jar lib/log4j-slf4j-impl-2.10.0.jar