I ran into this issue when trying to build an executable jar with maven in intellij 12. It turned out that because the java manifest file didn't include a class path the log4j properties file couldn't be found at the root level (where the jar file was executed from.)
FYI I was getting the logger like this:
Logger log = LogManager.getLogger(MyClassIWantedToLogFrom.class);
And I was able to get it to work with a pom file that included this:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>com.mycompany.mainPackage.mainClass</mainClass>
</manifest>
<manifestEntries>
<Class-Path>.</Class-Path> <!-- need to add current directory to classpath properties files can be found -->
</manifestEntries>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>