Hello, I'm writing because I was having issues with the plugin. I looked through the documentation and couldn't find any fixes or issues raised. Discord told me it was an issue with me, so I came here to be safe. I am not sure what I am doing wrong, I did everything the guide told me to do and it was working, to an extent with some issues I'm raising today.

Video (this may help you see my side of the story): https://youtu.be/XwcHXYimnWI
(33) CustomPermissionMessages, AntiRain, PlaceholderAPI, SimpleGeyserVL, NametagEdit, GroundItems, LaggRemover, MultiWorld, ccInstantRespawn, PermissionsEx, NoteBlockAPI, ViaVersion, Vault, floodgate, ViaBackwards, BisectHosting, JukeBox, ViaRewind, WorldEdit, Essentials, ProtocolLib, WorldGuard, ServerListMotdSpigot, Citizens, ChatItem, SetRankPEX, TabList, WG-GUI, EssentialsChat, Geyser-Spigot, CitizensGUI, DecentHolograms, CommandDoesNotExist

Plugin Version: 4.5.8

Permissions EX (permissions.yml):
https://pastebin.com/CpZ8Mx75

NametagEdit (groups.yml):
https://pastebin.com/CdavbAe5

NametagEdit (config.yml):
https://pastebin.com/7vTPmiCF

Issue: Name Tag is flashing the default Minecraft username everytime the RefreshInterval kicks in.
Issue 2: Name Tag is displaying the default Minecraft username between rank (group) changes.

Reproduce:
Simply install the plugin, match my config and do what I did in the video.

WATCH THE ENTIRE VIDEO BEFORE REPLYING (IT EXPLAINS MY GOAL)

Issue: Name Tag is flashing the default Minecraft username everytime the RefreshInterval kicks in.

This is currently expected, since refresh clears all the NTE data and then reapplies things. Refresh system should not be used to update ranks anyway.

Issue 2: Name Tag is displaying the default Minecraft username between rank (group) changes.

My first question would be, why are you using such an old plugin? Of course it works, but there are so much better plugins, maintained, user-friendly, etc. And that would fix your issue ;)
Anyway, NameTagEdit uses an API event from PEX to handle group change. Event is received since the nametag is completely removed after the command execution. However, permissions seem to be "missing", no new nametag is immediately applied, so I don't really know.

What old plugin are you referring to? I'm using PEX because PEX has no issues on it's side. LuckPerms breaks every update and I don't know of any others that is reliable or good like PEX.

I've tried TAB for name tags but that has a lot of issues for Bedrock clients (Geyser).
There are some others I tried but nothing really seems to be working.

I got a junk method to fixing this so it's fine lol. I legit am just running /nametagedit 3 seconds upon someone joining. It's not the best combat but it works and if it works, it works.