Jeg løste mit problem ved at ændre basisstien. Det fungerer fint.
Min anden klasse,
@ConditionalOnProperty(name = "embedded", havingValue = "true", matchIfMissing = true)
@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(entityManagerFactoryRef = "dataSyncEntityManagerFactory", transactionManagerRef = "dataSyncTransactionManager", basePackages = {
"kgfsl.rms.datasync" })
public class JPADataSyncConfig {