The warp delay is clearly set as 4, but neither the console nor the play in-game waits 4 seconds before actually warping or tp-ing.

# The delay, in seconds, required between /home, /tp, etc.
teleport-cooldown: 4

# The delay, in seconds, before a user actually teleports. If the user moves or gets attacked in this timeframe, the teleport is cancelled.
teleport-delay: 4

# The delay, in seconds, a player can't be attacked by other players after they have been teleported by a command.
# This will also prevent the player attacking other players.
teleport-invulnerability: 4

# Whether to make all teleportations go to the center of the block; where the x and z coordinates decimal become .5
teleport-to-center: true

edit by @triagonal: fixed code formatting

This is the full config. (Changed to txt from yml to upload)
config (2).txt

The console doesn't take delay into account when warping or teleporting other players.

This could be caused by your permission settings. If you're opped or have '*' in your permissions, then you're inheriting essentials.teleport.timer.bypass which bypasses the teleport delay. Could you double check to make sure your permissions are correct?

where are the permissions?

I'm using Spigot, and the permissions in the config file when i deop myself, and doesn't work even if i set use-bukkit-permissions to false. Every command i use says you do not have access to this command when i'm deopped.

Right, but if you're opped then you'll inherit the bypass permission. I've found that permissions changes (for player-commands permissions) sometimes require a server restart / player relog to take effect. Try setting up your permissions via player-commands in the config, restarting, and then trying it again.

alright, thanks.