I don’t really think that you have a Gradle problem. I am able to use the build.gradle you provided (minus the database dependencies) along with code from a standard Spring Boot Hello World example and I can access it as would be expected once deployed to Bluemix.
I think you’re dealing with either a Bluemix issue or a specifically a configuration in your application that isn’t compatible with the buildpack in Bluemix that you’re using. I don’t know that I can offer any other advice unless you can reproduce the same issue with a small sample project that you can share in its entirety. Even then, you might have much better luck with either Bluemix support or the Spring Boot community.