Spigot 1.10.2 server GM some permissions not working

Hi, I'm working on a small server running Spigot 1.10.2 using around 25 plugins, and i'm having a bit of trouble with some GroupManager permissions. Most of the permissions work, however there are a few that do not. For example, when using the plugin ReflectChat, I cannot use /clean (a command meant to clear the chat) even when in a GM group with the required permission node; rc.clean. The server denies access to the command in a way identical to as if I didn't have the correct permission. When using /manglistp to see the permissions my group has, it say's i have the right permission. I have tried using /mangaddp to add the permission to the globalgroups group, and the group itself. I have this problem with these plugins/permissions:

Essentials: essentials.firework
Essentials: essentials.tp
Grief Prevention: All (griefprevention.*)
ReflectChat: All (rc.*)
Holographic Displays: All (holograms.*)

Here is my globalgroups.yml and my groups.yml that is inherited in all worlds:
globalgroups.yml: http://pastebin.com/gBBYpegZ
groups.yml: http://pastebin.com/URDBy3R4

I have checked each file with this tool, which said that there were no errors:
wiki.ess3.net/yaml/

Thank you in advance for your help!!!