Basically me and my friend made a server and we successfully got it working. We are using a plugin called PermissionsEx and everything was working fine. then another friend joined and we wanted to make them moderator so I went to the permissions file and added her name to the list but it would'nt work. So then I just removed her name but then me and my friend lost our ranks, I then tried to return everything to as it was before but it just would'nt work. Then my friend did /plugins and found that the plugin was red. I dont know if its to do with the folder or the plugin. All the other plugins worked and we don't think there can be a clash of any sort. We are hoping to make this server public soon and we really do want it sorted ^^.
You probably just had a problem with your permissions.yml file, which could've easily been fixed Also, instead of double-posting please use the edit button at the bottom of your post.