No ManagedType on Spring Boot @EnableAutoConfiguration

I have a problem that started happening today on a code that was previously working and I can't figure out the cause...

My code has 4 different database connections and they were apparently working... But now, if I have more than 1 configured by @EnableAutoConfiguration I start seeing all kinds of "No ManagedType" errors...

Here's two of the persistence configurations:

PersistenceMailserver.class

@Configuration
@EnableTransactionManagement
@EntityScan(basePackages = {"org.cidb.restentre.mailserver.entities"})
@EnableJpaRepositories(entityManagerFactoryRef = "emfMailserver", transactionManagerRef = "tmMailserver", basePackages = {"org.cidb.restentre.mailserver.repositories"})
class PersistenceMailserver {
    @Primary
    @Bean(name="dsMailserver")
    DataSource dataSource() {
        BasicDataSource dataSource = new BasicDataSource();
        dataSource.setUrl("jdbc:mysql://host:3306");
        dataSource.setUsername("user");
        dataSource.setPassword("pass");
        dataSource.setDriverClassName("com.mysql.jdbc.Driver");
        return dataSource;
    }

    @Primary
    @Bean(name="emfMailserver")
    LocalContainerEntityManagerFactoryBean entityManagerFactoryBean() {
        LocalContainerEntityManagerFactoryBean entityManagerFactoryBean = new LocalContainerEntityManagerFactoryBean();
        entityManagerFactoryBean.setDataSource(dataSource());
        entityManagerFactoryBean.setJpaVendorAdapter(new EclipseLinkJpaVendorAdapter());

        entityManagerFactoryBean.setPersistenceXmlLocation("classpath:META-INF/mailserver-persistence.xml");

        Properties jpaProperties = new Properties();
        jpaProperties.put("eclipselink.weaving", "false");
        jpaProperties.put("eclipselink.logging.level", "SEVERE"); // SEVERE / FINEST

        entityManagerFactoryBean.setJpaProperties(jpaProperties);
        entityManagerFactoryBean.afterPropertiesSet();

        return entityManagerFactoryBean;
    }

    @Primary
    @Bean(name="tmMailserver")
    JpaTransactionManager transactionManager() {
        JpaTransactionManager transactionManager = new JpaTransactionManager();
        transactionManager.setEntityManagerFactory(entityManagerFactoryBean().getNativeEntityManagerFactory());
        return transactionManager;
    }
}

PersistenceIntegrator.class

@Configuration
@EnableTransactionManagement
@EntityScan(basePackages = {"org.cidb.restentre.integrator.entities"})
@EnableJpaRepositories(entityManagerFactoryRef = "emfIntegrator", transactionManagerRef = "tmIntegrator", basePackages = {"org.cidb.restentre.integrator.repositories"})
class PersistenceIntegrator {

    @Bean(name="dsIntegrator")
    DataSource dataSource() {
        BasicDataSource dataSource = new BasicDataSource();
        dataSource.setUrl("jdbc:mysql://someotherhost:3306");
        dataSource.setUsername("user");
        dataSource.setPassword("pass");
        dataSource.setDriverClassName("com.mysql.jdbc.Driver");
        return dataSource;
    }

    @Bean(name="emfIntegrator")
    LocalContainerEntityManagerFactoryBean entityManagerFactoryBean() {
        LocalContainerEntityManagerFactoryBean entityManagerFactoryBean = new LocalContainerEntityManagerFactoryBean();
        entityManagerFactoryBean.setDataSource(dataSource());
        entityManagerFactoryBean.setJpaVendorAdapter(new EclipseLinkJpaVendorAdapter());

        entityManagerFactoryBean.setPersistenceXmlLocation("classpath:META-INF/integrator-persistence.xml");

        Properties jpaProperties = new Properties();
        jpaProperties.put("eclipselink.weaving", "false");
        jpaProperties.put("eclipselink.logging.level", "SEVERE"); // SEVERE / FINEST

        entityManagerFactoryBean.setJpaProperties(jpaProperties);
        entityManagerFactoryBean.afterPropertiesSet();
        return entityManagerFactoryBean;
    }

    @Bean(name="tmIntegrator")
    JpaTransactionManager transactionManager() {
        JpaTransactionManager transactionManager = new JpaTransactionManager();
        transactionManager.setEntityManagerFactory(entityManagerFactoryBean().getNativeEntityManagerFactory());
        return transactionManager;
    }
}    

You can see they are pretty much the same and they were working last night... But now, if I run this code I get:

Caused by: java.lang.IllegalArgumentException: No [ManagedType] was found for the key class [org.cidb.restentre.integrator.entities.IntegratorCustomer] in the Metamodel - please verify     that the [Managed] class was referenced in persistence.xml using a specific <class>org.cidb.restentre.integrator.entities.IntegratorCustomer</class> property or a global <exclude-unlisted    -classes>false</exclude-unlisted-classes> element.
    at org.eclipse.persistence.internal.jpa.metamodel.MetamodelImpl.entityEmbeddableManagedTypeNotFound(MetamodelImpl.java:173)
    at org.eclipse.persistence.internal.jpa.metamodel.MetamodelImpl.managedType(MetamodelImpl.java:495)
    at org.springframework.data.jpa.repository.support.JpaMetamodelEntityInformation.<init>(JpaMetamodelEntityInformation.java:68)
    at org.springframework.data.jpa.repository.support.JpaEntityInformationSupport.getMetadata(JpaEntityInformationSupport.java:67)
    at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getEntityInformation(JpaRepositoryFactory.java:145)
    at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:89)
    at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:69)
    at org.springframework.data.repository.core.support.RepositoryFactorySupport.getRepository(RepositoryFactorySupport.java:172)
    at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.initAndReturn(RepositoryFactoryBeanSupport.java:239)
    at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.afterPropertiesSet(RepositoryFactoryBeanSupport.java:225)
    at org.springframework.data.jpa.repository.support.JpaRepositoryFactoryBean.afterPropertiesSet(JpaRepositoryFactoryBean.java:92)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1625)
    at org.springframework.beans.factory

Sometimes it complains about different classes when I run, which makes even harder to understand the probem...

The persistence.xml files are also pretty much the same (I wish I knew how to get rid of them, btw...)

<?xml version="1.0" encoding="UTF-8"?>
<persistence xmlns="http://ift.tt/UICAJV"
             xmlns:xsi="http://ift.tt/ra1lAU"
             xsi:schemaLocation="http://ift.tt/UICAJV http://ift.tt/O9YdEP" version="2.0">
    <persistence-unit name="puMailserver" transaction-type="RESOURCE_LOCAL">
        <provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
        <exclude-unlisted-classes>false</exclude-unlisted-classes>
    </persistence-unit>
</persistence>    

All they have different from each other is the persistence-unit name...

Any ideas?

Thanks!