your group.yml is fine but your globalgroups.yml is not
my globalgroups.yml file:
g:bukkit_default:
permissions:
- bukkit.broadcast.user
- -bukkit.command.plugins
g:essentials_default:
permissions:
- essentials.help
- essentials.helpop
- essentials.list
- essentials.motd
- essentials.rules
- essentials.spawn
- essentials.jail.allow.help
- essentials.jail.allow.helpop
- essentials.jail.allow.rules
/help is from essentials plugin so you should have it under g:essentials_default
For /thru, it is worldedit command and its permission is:
worldedit.navigation.thru.command
add this under g:essentials_default too
so it will be like:
g:essentials_default:
permissions:
- essentials.help
- essentials.helpop
- essentials.list
- essentials.motd
- essentials.rules
- essentials.spawn
- essentials.jail.allow.help
- essentials.jail.allow.helpop
- essentials.jail.allow.rules
- worldedit.navigation.thru.command