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Do you mean that you get the message "This is a valid URL but it doesn't look like JIRA" in the Jenkins configuration section for the plugin?
If yes you can ignore it, I get the same warning but it doesn't hinder the plugin from working.
To verify that it's working without messing around with comments and Issue workflow you could add a JIRA version parameter to your job (as described here: https://wiki.jenkins-ci.org/display/JENKINS/JIRA+Plugin) and see if the Plugin loads and offers you the versions from your JIRA project when you run the build.