Hmm weird. Not sure how you are producing this. I literally copied and pasted your config and items.yml into mine and it works fine.

Are you using spigot 1.9? If you are you fully up to date? Check with /version

Otherwise I will continue to look into this. So weird.. lol I have never seen this before.

Also please make sure a file called FirstJoin.yml is being created and players names are being stored in it perworld. If you are using linux there could be a permission issue with ItemJoin writing to said .yml file. Just a hunch though. Not really sure lol.

Okay first off your global settings look like this right?

Global-Settings:
First-Join:
FirstJoin-Mode-Enabled: true
Under each item do you have First-Join-Item: true ?

Example:

world:
items:
first-item:
id: WOOD_SWORD
slot: 1
commands-action: RIGHT_CLICK_AIR, RIGHT_CLICK_BLOCK, LEFT_CLICK_AIR
commands-cooldown: 5
First-Join-Item: true

If you are still having problems please post your config.yml and items.yml in a pastebin.com and link it to me.

Has this issue been fixed for you?

If you are still having this issue please download ItemJoin v2.8 and reopen this if you are still experiencing these problems.. Thanks!