People who're joining (player1) after you joined (player2) will see the you (player2) in vanish, despite he's not. Tested as OP with negotiated permission essentials.silentjoin.vanish and config section regarding this below.

EssentialsX version (/essentials):
b501

Server software (/version):
CraftBukkit version git-Spigot-596221b-2c5c611 (MC: 1.12) (Implementing API version 1.12-R0.1-SNAPSHOT)

EssentialsX config (if applicable):
allow-silent-join-quit: true

This appears to be caused by the bug in #1764.

I have a bit different issue in my case every admin when join server is automatically vanished. And I have to use command /vanish 2 times to be not vanished xD

Same as @arturek1666 - on my server we have an alias, /vfix, that runs /vanish twice to ensure that staff are visible or invisible as needed.

Yes i have the same issue, i need to enable vanish, and disable to actually be not vanished on join

That'd be amazing @Azewilous.

I can put some time into finding a fix for this if it's still needed.