If allow-silent-join-quit: true & if I'm OP, I'm always vanished on join but I wouldn't that.
Could you add option to disable essentials.silentjoin.vanish for OP please ?

I will test with this permission but with an other permission the negative permission doesn't work (-essentials.afk.auto

I have tested, it doesn't work :/

Using Essentials vanish functionality is not really recommended, as the information as to where you are, even if vanished, is still being sent to clients. Modified clients or "hacks" could most likely still see you. Look into VanishNoPacket for proper vanishing functionality.
Why did you negate essentials.afk.auto? What does that have to do with anything?

Just! I doesn't use essentials vanish, I use SuperVanish, but when I use allow-silent-join-quit, I'm automatically vanished... because I'm OP.
When I'm vanished (with supervanish) I'm spotted because of auto afk. It's enabled for players, but I'm OP and I have this permission automatically like silentjoin.vanish

Negate the permission (use permissions.yml if you don't have a permissions plugin).

I founded the cause of this problem after some test.
If I have the permission '*' (in user, not in group), the negative permissions in my Group are not included. So, I must use negative permissions in User to it works.

Firstly, please type /ess debug then try log in with the player who is automatically vanished. Then, please Pastebin your server log.

Steps:

1. Open logs directory in server directory.
2. Find and open a file called latest.log.
3. Go to www.pastebin.com.
4. Copy all latest.log contents and paste into the big text area.
5. Copy & paste the URL in your browser into a reply here.