I have 2 Spring Boot (1.4.1-RELEASE) console applications using Logback. Both configuration files are more or less identical, are located in my /src/main/resources
I know it is somewhat old, but i had the same issue and figured it out... so the reason is simply that you have a logback.xml on your classpath (somewhere, not necessarily in your project which you start, in my case it was a dependency).
Take a look here: org.springframework.boot.logging.AbstractLoggingSystem.initializeWithConventions(LoggingInitializationContext, LogFile)
set a breakpoint, then you will see.
If spring boot doesn't find any logback configurations ("logback-test.groovy", "logback-test.xml", "logback.groovy", "logback.xml") on the classpath, logback-spring.xml will be picked up.