I had to downgrade to version 3.4 because all the above versions are lagging my server very hard.

version 3.4:
https://puu.sh/rnlPI.png

version 3.7:
https://puu.sh/rnlRv.png

I will continue to look into this but there is no changes between v3.4 and v3.7's core code. So I do not know why there is a lag reduction. Ill post back when I get more information.

This should be fixed as of v3.8 and it has been uploaded. You can pick it up here; https://www.spigotmc.org/resources/itemjoin.12661/download?version=118664

Sadly I'm still having lag https://puu.sh/rIPF7.png

items.yml
https://puu.sh/rIVN6.yml

I'm going to try force compiling with Java 7 this time along with a few bug fixes and cut the code down a bit more for v3.9, but other than that if it still causes lag that will be something I will have to take into consideration when developing v4.0.

Can I ask, what version of java is installed on your system? If you can get the exact version that would be great but if you can't just tell me java 7 or 8.

Mine is Java 8 101. Then on my main system its Java 7 76 with no lag from ItemJoin on each system.