I was finally able to test the new ItemJoin release, but I still get the messages:
[ItemJoin Please contact the plugin developer immediately!
[ItemJoin This means your custom map will not be rendered!
[ItemJoin Something has gone wrong with the maps!

My config: http://pastebin.com/7D9CkNCw
My items.yml: http://pastebin.com/R3ka97Bc
I did not edit the language file

I figured out that it's just something with the default config, if I remove every item from the list except the first one, it's working fine.

Nope, I changed the maps before I removed the items

Hm... I will look into this again but I cant seem to replicate it. This is because you removed the map item so it doesnt have to render maps to the error never appears.

This has been fixed as of ItemJoin v3.5 and it has been released, I have decided to temporarily remove the custom maps item until spigot fixes their shit.

You can grab it here; https://www.spigotmc.org/resources/itemjoin.12661/download?version=107086