Websphere use a classloader for default for each EAR. If you have several Web modules or EJB modules and several files for log4j, only one is loaded by the classloader.
See A Powerful, Easy-to-Use Logging System for configure log4j with several projects in a EAR.
# Set root logger level to INFO and appender to STDOUT.
log4j.rootLogger=INFO, STDOUT
#------------------------------------STDOUT-----------------------------------#
# STDOUT is set to be a ConsoleAppender.
log4j.appender.STDOUT=org.apache.log4j.ConsoleAppender
# STDOUT uses PatternLayout.
log4j.appender.STDOUT.layout=org.apache.log4j.PatternLayout
log4j.appender.STDOUT.layout.ConversionPattern=%d %-5p (%c.java:%L).%M - %m%n
log4j.appender.STDOUT.Encoding=UTF-8
#-----------------------------------------------------------------------------#
# Specify the logging level for loggers from other libraries
log4j.logger.org.apache.commons.beanutils.BeanUtils=DEBUG
log4j.logger.org.apache.struts.action=DEBUG
log4j.logger.org.apache.struts.tiles=DEBUG
log4j.logger.org.apache.struts.util.ModuleUtils=DEBUG
log4j.logger.org.apache.struts.util.RequestUtils=DEBUG
log4j.logger.org.apache.struts.util.PropertyMessageResources=ERROR
log4j.logger.com.ibm._jsp=DEBUG
May you are missing the log4j.logger.
prefix for each particular package.
See more of log4j in http://logging.apache.org/log4j/1.2/manual.html