This is fixed in version 1.6 of the plugin.
<groupId>org.codehaus.mojo</groupId>
<artifactId>jaxb2-maven-plugin</artifactId>
<version>1.6</version>
Quick note though, I noticed that the first iteration output was being deleted. I fixed it by adding the following to each of the executions.
<removeOldOutput>false</removeOldOutput>
<clearOutputDir>false</clearOutputDir>
Here is my full working example with each iteration outputting correctly. BTW I had to do this due to a duplicate namespace problem with the xsd's I was given. This seems to resolve my problem.
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>jaxb2-maven-plugin</artifactId>
<version>1.6</version>
<executions>
<execution>
<id>submitOrderRequest</id>
<goals>
<goal>xjc</goal>
</goals>
<configuration>
<extension>true</extension>
<schemaDirectory>src/main/resources/xsd/</schemaDirectory>
<!-- <schemaFiles>getOrderStatusResponse.xsd,quoteShippingRequest.xsd,quoteShippingResponse.xsd,submitOrderRequest.xsd,submitOrderResponse.xsd</schemaFiles> -->
<schemaFiles>submitOrderRequest.xsd</schemaFiles>
<bindingDirectory>${project.basedir}/src/main/resources/xjb</bindingDirectory>
<bindingFiles>submitOrderRequest.xjb</bindingFiles>
<removeOldOutput>false</removeOldOutput>
<clearOutputDir>false</clearOutputDir>
</configuration>
</execution>
<execution>
<id>submitOrderResponse</id>
<goals>
<goal>xjc</goal>
</goals>
<configuration>
<extension>true</extension>
<schemaDirectory>src/main/resources/xsd/</schemaDirectory>
<!-- <schemaFiles>getOrderStatusResponse.xsd,quoteShippingRequest.xsd,quoteShippingResponse.xsd,submitOrderRequest.xsd,submitOrderResponse.xsd</schemaFiles> -->
<schemaFiles>submitOrderResponse.xsd</schemaFiles>
<bindingDirectory>${project.basedir}/src/main/resources/xjb</bindingDirectory>
<bindingFiles>submitOrderResponse.xjb</bindingFiles>
<removeOldOutput>false</removeOldOutput>
<clearOutputDir>false</clearOutputDir>
</configuration>
</execution>
</executions>
</plugin>