Example:
org.jvnet.jaxb2.maven2
you should change that to define the plugin only once and do twice execution areas...like the following...and the generateDirectory should be set (based on the docs)..
org.jvnet.jaxb2.maven2
maven-jaxb2-plugin
0.7.1
firstrun
generate
target/gen1
src/main/resources/dir1
schema1.xsd
schema1.package
secondrun
generate
target/gen2
src/main/resources/dir2
schema2.xsd
schema2.package
It seemed to me that you are fighting against single artifact rule of maven...may be you should think about this.