Here is a problem/issue found while using Sonar in a Maven 3 Java JS project using JENKINS
I hope I can help you by pointing out to you the first paragraph of this documentation:
It sais "...Therefore, for a multi-language project, the property usually has to be overridden to: sonar.sources=src. Note that this property can only be set in the pom file. It's not possible to set it via the command line."
http://docs.codehaus.org/display/SONAR/Analyzing+with+Maven#AnalyzingwithMaven-AnalyzingaMulti-languageProject
Good Luck!