The reason must be somewhere else. Using only Spring Boot 1.2.2 out of the box with no configuration, it Just Works. Have a look at this repo – can you get it to break?
https://github.com/konrad-garus/so-yaml
Are you sure the YAML file looks exactly the way you pasted? No extra whitespace, characters, special characters, mis-indentation or something of that sort? Is it possible you have another file elsewhere in the search path that is used instead of the one you’re expecting?