Has Spring-boot changed the way auto-increment of ids works through @GeneratedValue?

Spring Boot 2.0 uses Hibernate 5.2 (https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.0-Release-Notes).
Hibernate changes its GeneratedType.AUTO strategy since 5.2. Any database that does not support sequences natively (e.g. MySQL), they use the TABLE generator instead of IDENTITY. (https://hibernate.atlassian.net/browse/HHH-11014)

That's why GeneratedType.AUTO does not work as you expected.

As Andrew has pointed out in the comment, if you don't want the id to be incremented while values are created in other tables, you can specify your ID like this:

@Id
@GeneratedValue(
    strategy= GenerationType.AUTO,
    generator="native"
)
@GenericGenerator(
    name = "native",
    strategy = "native"
)
private Long id;

Doing this will make each table has its unique id beginning with 1,2,3 ... and so on.