Plugin Help Permissions aren't working? Pex

I'll keep this short, players cannot use commands, I remade this code multiple times in different layouts. Prefixes work and I can change players ranks but they cannot build, use anything, and two messages show upon using commands like /spawn: "You do not have access to that command." and "You don't have permission." Plugins: AutoBroadcaster, PermissionsEx, NoCheatPlus, WorldEdit, AbsoluteWelcome, Essentials, EssentialsChat, EssentialsProtect, EssentialsAntiBuild, and EssentialsSpawn. Permissions: http://pastebin.com/GyC6w8TJ
Anyone know how to fix this? Thanks. [EDIT]: The permissions change from the normal

essentials.node
essentials.example

to this format

essentials.node essentials.example

upon pasting it into the permissions file, not sure if it matters.

 

try adding a - before every command rather then just plainly putting them in so:

- essentials.fly
- essentials.day
- etc
- etc
- etc