Problem/Bug Group Manager isn't saving group permissions

When I set all my 40+ groups permissions via /Mangaddp [group] [Perm],[Perm],[Perm] etc None of them saved their group permissions and they just arent working. Help??

 

@timtower

I've tried that. It says they have all the permissions but when a player tries to run a command they should have permissions for such as /me it displays "You do not have access to this command!"
These are a list of permissions im trying to give

essentials.afk, essentials.afk.auto, essentials.balance, essentials.balancetop, essentials.chat.color, esentials.chat.shout, essentials.chat.questions, essentials.getpos, essentials.mail, essentials.mail.send, essentials.me, essentials.seen, essentials.msg, essentials.msg.color, essentials.signs.use, essentials.list, essentials.motd, essentials.near, essentials.r, essentials.signs.use.buy, essentials.signs.use.trade, essentials.signs.use.free, essentials.signs.use.warp, essentials.signs.use.gamemode, essentials.tpaccept, backpack.use