Spring Boot 2.0 Hibernate 5 EhCache 3 with JCache

I think I found the cause of the issue - you didn't specify a location of the ehcache.xml file:

spring:
  jpa:
    properties:
      hibernate:
        javax.cache:
          provider: org.ehcache.jsr107.EhcacheCachingProvider
          uri: classpath:ehcache.xml
        cache:
          use_second_level_cache: true
          region.factory_class: jcache
          use_query_cache: true

in this case Hibernate creates a cache with default configuration. A fragment from my demo project log:

17:15:19 WARN [main] org.hibernate.orm.cache: HHH90001006: Missing cache[user] was created on-the-fly. The created cache will use a provider-specific default configuration: make sure you defined one. You can disable this warning by setting 'hibernate.javax.cache.missing_cache_strategy' to 'create'.