I used the old project I had in my Projects list. And it works there flawlessly.
For easier readability here are the results: Log4j configuration debug output in working project: **Start of LogManager static initializer *** configurationOptionStr=null ** End of LogManager static initializer DEBUG [org.apache.log4j.PropertyConfigurator] Parsing for [root] with value=[DEBUG, stdout]. DEBUG [org.apache.log4j.PropertyConfigurator] Level token is [DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Category root set to DEBUG. DEBUG [org.apache.log4j.PropertyConfigurator] Parsing appender named "stdout". DEBUG [org.apache.log4j.PropertyConfigurator] Parsing layout options for "stdout". DEBUG [org.apache.log4j.config.PropertySetter] Setting property [conversionPattern] to [%5p [%c] %m%n]. DEBUG [org.apache.log4j.PropertyConfigurator] End of parsing for "stdout". DEBUG [org.apache.log4j.PropertyConfigurator] Parsed "stdout" options. DEBUG [org.apache.log4j.PropertyConfigurator] Parsing for [org.apache.http.wire] with value=[DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Level token is [DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Category org.apache.http.wire set to DEBUG. DEBUG [org.apache.log4j.PropertyConfigurator] Handling log4j.additivity.org.apache.http.wire=[null] DEBUG [org.apache.log4j.PropertyConfigurator] Parsing for [org.apache.http] with value=[DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Level token is [DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Category org.apache.http set to DEBUG. DEBUG [org.apache.log4j.PropertyConfigurator] Handling log4j.additivity.org.apache.http=[null] DEBUG [org.apache.log4j.PropertyConfigurator] Parsing for [stupidClass] with value=[DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Level token is [DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Category stupidClass set to DEBUG. DEBUG [org.apache.log4j.PropertyConfigurator] Handling log4j.additivity.stupidClass=[null] DEBUG [org.apache.log4j.PropertyConfigurator] Parsing for [jobManager] with value=[DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Level token is [DEBUG]. DEBUG [org.apache.log4j.PropertyConfigurator] Category jobManager set to DEBUG. DEBUG [org.apache.log4j.PropertyConfigurator] Handling log4j.additivity.jobManager=[null] DEBUG [org.apache.log4j.PropertyConfigurator] Finished configuring. Log4j configuration debug output in NOT working project: log4j: Trying to find [log4j.xml] using context classloader sun.misc.Launcher$AppClassLoader@2827f394. log4j: Trying to find [log4j.xml] using sun.misc.Launcher$AppClassLoader@2827f394 class loader. log4j: Trying to find [log4j.xml] using ClassLoader.getSystemResource(). log4j: Trying to find [log4j.properties] using context classloader sun.misc.Launcher$AppClassLoader@2827f394. log4j: Using URL [file:/home/min/ucng/ucng_java/sBorgJava/src/logging/log4j.properties] for automatic log4j configuration. log4j: Reading configuration from URL file:/home/min/ucng/ucng_java/sBorgJava/src/logging/log4j.properties log4j: Parsing for [root] with value=[DEBUG, stdout]. log4j: Level token is [DEBUG]. log4j: Category root set to DEBUG log4j: Parsing appender named "stdout". log4j: Parsing layout options for "stdout". log4j: Setting property [conversionPattern] to [%5p [%c] %m%n]. log4j: End of parsing for "stdout". log4j: Parsed "stdout" options. log4j: Parsing for [org.apache.http.wire] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category org.apache.http.wire set to DEBUG log4j: Handling log4j.additivity.org.apache.http.wire=[null] log4j: Parsing for [org.apache.http] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category org.apache.http set to DEBUG log4j: Handling log4j.additivity.org.apache.http=[null] log4j: Parsing for [stupidClass] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category stupidClass set to DEBUG log4j: Handling log4j.additivity.stupidClass=[null] log4j: Parsing for [jobManager] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category jobManager set to DEBUG log4j: Handling log4j.additivity.jobManager=[null] log4j: Finished configuring. log4j: Parsing for [root] with value=[DEBUG, stdout]. log4j: Level token is [DEBUG]. log4j: Category root set to DEBUG log4j: Parsing appender named "stdout". log4j: Parsing layout options for "stdout". log4j: Setting property [conversionPattern] to [%5p [%c] %m%n]. log4j: End of parsing for "stdout". log4j: Parsed "stdout" options. log4j: Parsing for [org.apache.http.wire] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category org.apache.http.wire set to DEBUG log4j: Handling log4j.additivity.org.apache.http.wire=[null] log4j: Parsing for [org.apache.http] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category org.apache.http set to DEBUG log4j: Handling log4j.additivity.org.apache.http=[null] log4j: Parsing for [stupidClass] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category stupidClass set to DEBUG log4j: Handling log4j.additivity.stupidClass=[null] log4j: Parsing for [jobManager] with value=[DEBUG]. log4j: Level token is [DEBUG]. log4j: Category jobManager set to DEBUG log4j: Handling log4j.additivity.jobManager=[null] log4j: Finished configuring. Classpath in working project: /home/min/netbeans-7.1.1/java/modules/ext/toplink/toplink-essentials.jar /home/min/netbeans-7.1.1/java/modules/ext/toplink/toplink-essentials-agent.jar /home/min/netbeans-7.0.1/ide/modules/ext/mysql-connector-java-5.1.13-bin.jar /home/min/netbeans-7.1.1/java/modules/ext/beansbinding-1.2.1.jar /home/min/ucng/javaLibs/eclipselink-2.3.2/jlib/eclipselink.jar /home/min/netbeans-7.1.1/java/modules/ext/eclipselink/javax.persistence-2.0.jar /home/min/netbeans-7.1.1/java/modules/ext/eclipselink/org.eclipse.persistence.jpa.jpql_1.0.0.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/commons-codec-1.4.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/commons-collections-3.2.1.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/commons-io-2.0.1.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/commons-lang-2.6.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/commons-logging-1.1.1.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/cssparser-0.9.5.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/htmlunit-2.9.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/htmlunit-core-js-2.9.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/httpclient-4.1.2.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/httpcore-4.1.2.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/httpmime-4.1.2.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/nekohtml-1.9.15.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/sac-1.3.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/serializer-2.7.1.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/xalan-2.7.1.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/xercesImpl-2.9.1.jar /home/min/ucng/javaLibs/htmlunit-2.9/lib/xml-apis-1.3.04.jar /home/min/netbeans-7.1.1/platform/modules/ext/junit-4.10.jar /home/min/netbeans-7.1.1/enterprise/modules/ext/javaee-api-6.0.jar /home/min/netbeans-7.1.1/enterprise/modules/ext/javaee-web-api-6.0.jar /home/min/netbeans-7.1.1/enterprise/modules/ext/javaee6-endorsed/javax.annotation.jar /home/min/netbeans-7.1.1/enterprise/modules/ext/javaee6-endorsed/jaxb-api-osgi.jar /home/min/netbeans-7.1.1/enterprise/modules/ext/javaee6-endorsed/webservices-api-osgi.jar /home/min/netbeans-7.1.1/java/modules/ext/AbsoluteLayout.jar /home/min/workspace/JDownloader/build/newBuild/update/dist/JDownloader.jar /home/min/ucng/javaLibs/json-lib-2.4-jdk15-javadoc.jar /home/min/ucng/javaLibs/json-lib-2.4-jdk15.jar /home/min/ucng/javaLibs/ezmorph-1.0.6.jar /home/min/ucng/javaLibs/commons-logging-1.1.1/commons-logging-1.1.1.jar /home/min/ucng/javaLibs/commons-logging-1.1.1/commons-logging-adapters-1.1.1.jar /home/min/ucng/javaLibs/commons-logging-1.1.1/commons-logging-api-1.1.1.jar /home/min/ucng/javaLibs/commons-beanutils-1.8.3/commons-beanutils-1.8.3.jar /home/min/ucng/javaLibs/commons-beanutils-1.8.3/commons-beanutils-bean-collections-1.8.3.jar /home/min/ucng/javaLibs/commons-beanutils-1.8.3/commons-beanutils-core-1.8.3.jar /home/min/ucng/javaLibs/commons-collections-3.2.1/commons-collections-3.2.1.jar /home/min/ucng/javaLibs/xom-1.2.7.jar /home/min/ucng/javaLibs/chainsaw-bundle/jakarta-oro-2.0.6.jar /home/min/ucng/javaLibs/chainsaw-bundle/jmdns.jar /home/min/ucng/javaLibs/chainsaw-bundle/log4j-1.3alpha-7.jar /home/min/ucng/javaLibs/chainsaw-bundle/log4j-chainsaw-2.0alpha-1.jar /home/min/ucng/javaLibs/chainsaw-bundle/log4j-optional-1.3alpha-7.jar /home/min/ucng/javaLibs/chainsaw-bundle/log4j-oro-1.3alpha-7.jar /home/min/ucng/javaLibs/chainsaw-bundle/log4j-smtp-1.3alpha-7.jar /home/min/ucng/javaLibs/chainsaw-bundle/log4j-xml-1.3alpha-7.jar /home/min/ucng/javaLibs/chainsaw-bundle/log4j-zeroconf.jar /home/min/ucng/javaLibs/chainsaw-bundle/xstream-1.1.2.jar /home/min/ucng/javaLibs/groovy-1.8.6/embeddable/groovy-all-1.8.6.jar /home/min/ucng/ucng_java/UCNG/build/classes/ Classpath in NOT working project: /home/min/ucng/ucng_java/sBorgJava/src/logging/ /home/min/ucng/javaLibs/httpcomponents-client-4.1.3/lib/commons-codec-1.4.jar /home/min/ucng/javaLibs/httpcomponents-client-4.1.3/lib/commons-logging-1.1.1.jar /home/min/ucng/javaLibs/httpcomponents-client-4.1.3/lib/httpclient-4.1.3.jar /home/min/ucng/javaLibs/httpcomponents-client-4.1.3/lib/httpclient-cache-4.1.3.jar /home/min/ucng/javaLibs/httpcomponents-client-4.1.3/lib/httpcore-4.1.4.jar /home/min/ucng/javaLibs/httpcomponents-client-4.1.3/lib/httpmime-4.1.3.jar /home/min/ucng/javaLibs/httpcomponents-client-4.1.3/lib/log4j-1.2.16.jar /home/min/ucng/javaLibs/commons-codec-1.6/commons-codec-1.6-javadoc.jar /home/min/ucng/javaLibs/commons-codec-1.6/commons-codec-1.6-tests.jar /home/min/ucng/javaLibs/commons-codec-1.6/commons-codec-1.6.jar /home/min/ucng/javaLibs/selenium-server-standalone-2.20.0.jar /home/min/ucng/javaLibs/scribe-1.3.0.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/pbapi-j2se.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/apache-mime4j-0.6.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/commons-codec-1.3.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/commons-codec-1.4.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/commons-lang-2.4.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/commons-logging-1.1.1.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/commons-validator-1.3.1.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/httpclient-4.0.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/httpclient-4.1.3.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/httpclient-cache-4.1.3.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/httpcore-4.0.1.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/httpcore-4.1.4.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/httpmime-4.0.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/httpmime-4.1.3.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/jcip-annotations-1.0.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/json-1.0.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/junit-4.9b2.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/log4j-1.2.16.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/signpost-commonshttp4-1.2.1.1.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/signpost-commonshttp4-1.2.1.2.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/signpost-core-1.2.1.1.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/signpost-core-1.2.1.2.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/signpost-jetty6-1.2.1.2.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/slf4j-api-1.6.1.jar /home/min/ucng/javaLibs/pbapi-full-1.4.0.91/dist/lib/default/slf4j-log4j12-1.6.1.jar /home/min/ucng/ucng_java/sBorgJava/build/classes/ Lines of code used in working project: System.setProperty("log4j.debug", "true"); PropertyConfigurator.configure("./../sBorgJava/src/logging/log4j.properties"); // <- notice the ./../ (points to same file) Lines of code used in NOT working project: 50+. Various. For the sake of it, I commented out everything except System.setProperty("log4j.debug", "true"); PropertyConfigurator.configure("./sBorgJava/src/logging/log4j.properties"); // <- notice the ./../ (points to same file) still got the NOT working results. I already tried adding random jars from working project to not working, but it didn't help.