1.) The version of the Resource.
v4.8
Config-Version: 6
2.) Version of the Spigot / Craftbukkit / Cauldron / ETC.
1.8.9 Spigot / Bukkit Server
3.) What is the problem that you are having?
I receive my items as normal on the hub world but when I got into any other world, put stuff in my inv and log out (of the world I'm in) I lose all the items that were in my inv in the world I logged out of.
Example: Log in (hub) go on survival, use kits (put stuff in my inv), log out (while in survival world), log back in (start in hub), go back to survival world, my inventory is completely empty.
4.) Post all your YAML / Configuration files, please include a Pastebin.com link.
config.yml: https://pastebin.com/9UfWzuHg
items.yml: https://pastebin.com/qRQDNfqh
5.) Post any error codes found in your console window if it pertains to this issue, please include a Pastebin.com link.
Console Error: https://pastebin.com/4EKtxacL

You have clear on world changed set in the config.yml so once you change worlds it will clear your inventory. I would recommend setting this to false and testing if this resolves your issue.

Did you also try to disable clear-on-join in the config.yml?
If you could upload a video that could visually show me what the issue is that would be great, or a test server that you are able to replicate the issue on so I could join and test it using the steps you provided.

However, if you disable clear-on-world-changed and clear-on-join and your items are still clearing it wouldn't be an issue with ItemJoin as those are the only functions that allow ItemJoin to clear any items.

EDIT: Closing due to inactivity, if you continue to have this issue please reopen this ticket.

ItemJoin v4.9 has been officially released; https://www.spigotmc.org/resources/itemjoin.12661/download?version=233044

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