My Spring boot app has this application structure:
in my case, the same problem had a slightly different cause - i had a class with a static instance variable (the old usual way we used to implement a Singleton pattern), into which i wanted to inject an entry from application.properties (probably the "static" thing was why the property could not be found - with no errors no anything :/).
moreover this class was in a totally different package from the class declared as @SpringBootApplication. i understood that package names and locations have to be taken into serious consideration with Spring Boot and automatic component scanning. my 5 cent