Class path entry missing in assemblies since maven 3

We have an EJB project along with some custom assemblies:

<project>
...
<name>test</name>
<packaging>ejb</packaging>
...
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>sender</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptors>
<descriptor>src/main/assembly/custom.xml</descriptor>
</descriptors>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

This creates a test.jar and a test-custom.jar. The first jar has its Class-Path entry filled in correctly in the manifest file, but the 2nd jar has no Class-Path entry. The <addClasspath>true</addClasspath> was added for the maven assembly plugin, the maven-ejb-plugin in the parent pom also has this property set to true.

This only happens with maven 3.0.3. With maven 2.2.1 both jars have their Class-Path filled in properly.