I'm also using JPA Metamodel generator and I don't have the problems you describe, maybe my configuration can help, I see some differences, the first one is maven-processor-plugin
org.bsc.maven
maven-processor-plugin
2.1.0
process
process
generate-sources
org.hibernate.jpamodelgen.JPAMetaModelEntityProcessor
org.hibernate
hibernate-jpamodelgen
4.3.4.Final
As you can see I had to add hibernate-jpamodelgen as dependency and the processor attribute.
I am not sure if build-helper-maven-plugin is necessary to add the directory of generated sources to your source path. I am not using it and it works for me but maybe it's because I am using the default output path for generated sources.