I have created a set of Java Rules and packed it in a jar file using (Java plug in 3.13.1) as a dependency. Then added to the plugin path in my Sonar Qube 5.0.1 local installation($SONAR_HOME/extensions/plugins).
Now I was able to see the rules through the web interface. Then I run the sonnar-runner scanner (2.4) to test the issues generated to the custom rules. but after a successful execution there are no issues shown in the project through the web interface.
There are no errors or warnings in the sonar.log.
i have created custom profile using http://docs.sonarqube.org/display/PLUG/Writing+Custom+Java+Rules+101 steps.
I have below versions for plugins.
Please make sure you're using same java plugin version :
1. in your "pom" -
2. under $SONAR_HOME/extensions/plugins