Hibernate DuplicateMappingException when debugging using JUnit

Hoping someone can help.

My project uses Spring, JPA (hibernate provider), and Hibernate hbm.xml files to map entities and named queries (I like having the mapping externalized). The Spring config is annotation driven. This application starts and runs fine. It also tests fine. All tests run and pass in the Maven runner using the ‘test’ goal. All tests run and pass using the JUnit runner.

The issue is when debugging tests. If I debug using the JUnit Runner, I get the following error:

Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: Duplicate query mapping <my-named-query>

I get it when debugging a single test method, a single test class, or all the test classes. But it does not happen when I simply run a test or I run multiple tests. It only happens when debugging. My tests start the Spring context via annotations on the test class.

@ActiveProfiles("test")
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = {ApplicationConfiguration.class})

Any thoughts? Thanks in advance.