I'm using logback in my project and also neo4j-server, I'm getting WARN from logback because of multiple logback.xml file found in classpath,
I think you should rename your file to neo4j-server-logback.xml or something like this.
I've posted a question on SO with more details
It is no longer supported to bundle Neo4j server as a whole in an application, other than for testing. However - we do actually no longer ship a logback.xml on the classpath, so this has been resolved :)