Since you haven't included details about how you've configured log4j, I can only gues that you've specified a relative path for the file that log4j is to use and you may not be able to find where it is putting it when running outside of eclipse.
Are you running with log4j.debug=true to see any debug output it might be giving you?
Joined: Aug 03, 2005
This is my log4j.properties placed in WEB-INF/Classes.
# Create two appenders, one called stdout and the other called rolling log4j.rootLogger=DEBUG, VDSConsole, VDSDebug, VDSInfo, VDSError, VDSWarn