I have a project that uses the maven-jaxb2-plugin. When the project
 is built during an Eclipse build, the plugin runs, but it ignores some 
(but not all) of the configuration parameters. In particular, I have 
some custom bindings and a binding plugin. I can tell that this is 
running, but the bindings are being ignored because the classes are 
being generated but in the wrong projects and some other substitutions 
aren't being done.
When run from RunAs->Maven generate-sources, everything works fine. Here's a segment from my POM:
  <build>
    <plugins>
      <plugin>
        <groupId>org.jvnet.jaxb2.maven2</groupId>
        <artifactId>maven-jaxb2-plugin</artifactId>
        <version>0.13.0</version>
        <dependencies>
          <dependency>
            <groupId>com.frequentz.iris.dscsa</groupId>
            <artifactId>com.frequentz.iris.dscsa.common</artifactId>
            <version>4.4.0.0</version>
          </dependency>
        </dependencies>
        <executions>
          <execution>
            <id>generate_epcis_beans</id>
            <goals>
              <goal>generate</goal>
            </goals>
            <configuration>
              <generateDirectory>${project.build.sourceDirectory}</generateDirectory>
              <schemaDirectory>${project.basedir}/schema</schemaDirectory>
              <schemaIncludes>
                <include>GS1US-epcis-dscsa-1_1.xsd</include>
              </schemaIncludes>
              <bindingIncludes>
                <include>jaxb-binding-dscsa.xml</include>
              </bindingIncludes>
              <extension>true</extension>
              <args>
                <arg>-Xepcis</arg>
                <arg>-Xepcis-templates=${project.build.sourceDirectory}</arg>
              </args>
              <plugins>
                <plugin>
                  <groupId>com.frequentz.iris.tools</groupId>
                  <artifactId>com.frequentz.iris.xml.tools</artifactId>
                  <version>1.0.0</version>
                </plugin>
              </plugins>
              <produces>
                <produce>com/frequentz/iris/dscsa/epcis/xml/impl/*.java</produce>
              </produces>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>