I have BungeecCord setup, and with the same permissions on each server, when I connect to the default (hub) server, it doesn't vanish me on join and announces when I join and leave. Even though I'm OP and have the same permissions for my group. It works on all the other servers. As well, my other staff don't have a problem with this. This has happened since the update to 3.18.3

Know what could be causing this issue?

I'd say your permissions aren't set up on there.

Here are permission files:
http://pastebin.com/QtxwKEMJ

Your indentation looks wonky. Regardless, let's try things out.

1. Confirm PEX is running.
2. In the VNP config set permtest to true
3. Do vanish reload in console
4. Join the server and type /permtest vanish.silentjoin

It says I don't have the permission. Hm...

The permtest command directly queries the permissions api in Bukkit. So, you don't have it. :(

Closing the ticket as it's resolved on this end.