When you rename a job group that is set to "Jobs marked for inclusion", all the jobs that were marked as belonging to that group lose their assigned group.
I think this is because job group membership is stored by name in the config.xml, rather than by a unique ID, so if the name changes the job is set to be a member of a non-existent group.
emsa23 does not longer work on the plugin. Feel free to take thios issue and to propose a pull request, I am ready to help with reviews