Реших проблема си, като промених основния път. Работи добре.
Моят втори клас,
@ConditionalOnProperty(name = "embedded", havingValue = "true", matchIfMissing = true)
@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(entityManagerFactoryRef = "dataSyncEntityManagerFactory", transactionManagerRef = "dataSyncTransactionManager", basePackages = {
"kgfsl.rms.datasync" })
public class JPADataSyncConfig {
