NoUniqueBeanDefinitionException: No qualifying bean of type [javax.persistence.EntityManagerFactory] is defined: expected single matching bean

I think you should be naming your LocalContainerEntityManagerFactoryBean's in both configurations. So it should look like:

@Bean(name = "nextGenEntityManagerFactory")
@Primary
public LocalContainerEntityManagerFactoryBean nextGenEntityManagerFactory() {

for the first one and

@Bean(name = "gatcLimsEntityManagerFactory") 
public LocalContainerEntityManagerFactoryBean gatcLimsEntityManagerFactory() {

for the second.