1.) v4.7
2.) Spigot 1.8.8
3.) https://imgur.com/a/La7AR
4.) https://pastebin.com/uq9zA8vd

Please use the latest snapshot; http://ci.craftationgaming.com/job/ItemJoin/107/artifact/target/ItemJoin-4.8-SNAPSHOT.jar (This is safe to use, this snapshot has only seen bug fixes and no major changes)

This should fix your issue, if it does not please post your items.yml and config.yml in a pastebin.com and send me the link.

Let me know :)

ItemJoin v4.8 has been officially released containing this bug fix for official usage.
You can grab it here; https://www.spigotmc.org/resources/itemjoin.12661/download?version=223327

Please read the changelog as the documentation has not been updated yet;
https://www.spigotmc.org/wiki/recent-changes