All prefixes and chat colors stop working when permissions updated

Hello guys. I have this strange issue as of opening a new mc server. It seems that every time I update the permissions in pex the colors in the chat stop working as do the prefixes. When the permissions are updated in McMyAdmin the chat also gets messed up. For example: I add essentials.tpa to the group Everyone, and as soon as I do that, all prefixes and chat colors stop working. Server is on linux opensuse running with McMyAdmin. All the perms are updated through McMyAdmin as it is exporting it to PermissionsEx. Also using EssentialsChat