This is actually an issue with gitlab-hook design. It searchs for projects with matching repository url, and apart for the branch and refspec checks, no other configuration item from git-plugin is considered. Neither ignored users, nor ignored paths nor anything else.
The reason behind is that is implemented on ruby, and there is no actual triggers on jruby-jenkins, so the plugin is actually a jenkins RootAction. I've done some steps toward it, but it's not yet ready, so this will take some time to get fixed.