Everytime I load the plugin it says that all the perms the plugin contains duplicated but it says it 100% loaded. When I type /perms none of the perms show up. Any Ideas?

What exactly is the message you see?

EnhancedBanSystem was compiled successfully in 2562ms
EnhancedBanSystem has replaced the 'ban' command previously registered by ServerArmour
EnhancedBanSystem has replaced the 'unban' command previously registered by ServerArmour
[Enhanced Ban System] You must enable at least one Ban System to use this plugin!
Unloaded plugin Enhanced Ban System v5.2.4 by Reneb/Slut
Loaded plugin Enhanced Ban System v5.2.4 by Reneb/Slut

Those are the commands, not permissions. Only one plugin can utilize each command, and in your case, Server Armour registered the same commands before you loaded this plugin. You can safely ignore them, the commands just won't work via Server Armour unless you change them in one of the plugins to be unique.

Ah ok. Thank you