Information

Full output of /ess version:

https://pastebin.com/H1mYrjZM

Server log: https://pastebin.com/DP0CFRi0

EssentialsX config: https://pastebin.com/jxN8jgMx

Details

Description
Server running version : Paper 1.16.3

When a player logs in he receives the welcome kit twice.

Steps to reproduce
Go to the config file to EssentialsAntiBuild part and set use to true.

Like this :

    # Should people without the essentials.build permission be allowed to use items?
    # Set true to disable using for those people.
    # Setting to false means EssentialsAntiBuild will never prevent you from using items.
    use: true

Now delete your playerdata to simulate a new player and see.

Expected behavior
The player have not the permission to drop and pickup items when is logs in, the kit is overflowed.

Unable to replicate this in the way you described, seems to work just fine.