Feed back from egetchel@redhat.com in a recent Fuse enablement session:

This seems specific to JBDS 11.x as it is not a problem in 10. Typical scenario - I start a new project in Eclipse and it defaults to a JRE enviornment. This gets picked up at runtime. I add the JDK to Eclipse. Normally, I can go into the project configuration and change the compile and runtime to use the new JDK. In Eclipse 11, we could not find any option to do this, and no matter what we did, running the Spring Boot project still defaulted back to the JRE. The only way to force Eclipse to use the JDK was to go into Eclipse and delete the reference to the JRE, so that only a single JDK existed.