Problem/Bug PEX "Expanding Permissions" and Lags Server

I am an admin on a local server for my friends and I am trying to use Permissions Ex to play nice with JEsssentials. There are four all-encompassing permissions that I gave myself:
- modifyworld.*
- jessentials.*
- vault.admin
- lagg.*

These work correctly and giving myself the admin role ensures that I am able to modify anything I need to. However, whenever I load into the world, it "expands" these permissions under my specific user into a 300+ line mess that lags the server. Ex:

users:
82cde5eb-d543-4db1-9721-7f8c18f6ed96:
group:
- admin
options:
name: Am_Snek
worlds:
world:
permissions:
- jessentials.gms
- jessentials.motd
- jessentials.heal.others
- jessentials.enchant.frost_walker
...

Even if I delete it, it simply returns whenever I load back in. A solution for this was to put the admin perms under my specific username:

worlds:
world:
permissions:
- modifyworld.*
- jessentials.*
- vault.admin
- lagg.*

This prevented it from spamming the console but took away perms from all of my friends (for whatever reasons). The most pressing issue from this is whenever I attempt to go to the nether, in which I immediately get an internal server error and am kicked and when I rejoin it crashes the server about 50% of the time. This is likely because it transfers those 300+ perms to world_nether. Is there a way to fix this? Full permission logs in attached.

What it becomes when loading in:


"Fix" (fixes the issue but removes friends' perms):


What it was originally (before expanding perms):