Bone hunter is right, group manager causes more problems then it's worth! Use Permissions Ex and you'll be happier. And look here for everything you need permissions based https://github.com/PEXPlugins/Permissio ... Pex-basics

And again:
DONT use group manager.That plugin is so retarded !
Use permissionsEx !
Then u should have no problems with the warps !
And why u have - -essentials.warp that means you dont allow using warps for defaults.
Replace it with: - essentials.warp

groups:
Guest:
default: true
permissions:
- -essentials.warp
- -essentials.warp.list
- -essentials.spawn
inheritance:
- g:groupmanager_default
- g:bukkit_default
- g:essentials_default
info:
prefix: '&8[Guest] &f'
build: true
suffix: ''
Member:
default: false
permissions: []
inheritance:
- guest
- g:essentials_builder
- g:towny_builder
info:
prefix: '&b[Member] &f'
build: true
suffix: ''
Moderator:
default: false
permissions: []
inheritance:
- member
- g:groupmanager_moderator
- g:bukkit_moderator
- g:essentials_moderator
- g:towny_moderator
- g:vanish_moderator
info:
prefix: '&6[Moderator] &f'
build: true
suffix: ''
Administrator:
default: false
permissions: []
inheritance:
- moderator
- g:groupmanager_admin
- g:bukkit_admin
- g:essentials_admin
- g:towny_admin
- g:vanish_admin
info:
prefix: '&9[Administrator] &f'
build: true
suffix: ''
Owner:
default: false
permissions:
- '*'
- -vanish.*
inheritance:
- admin
info:
prefix: '&4[Owner] &f'
build: true
suffix: ''