Bug Report

Type /ver NametagEdit and post the output.
4.4.10

What version of Bukkit/Spigot/PaperSpigot are you using? Type /ver
This server is running CraftBukkit version git-Spigot-dcd1643-e60fc34 (MC: 1.12.2) (Implementing API version 1.12.2-R0.1-SNAPSHOT)

What plugins are you using? Type /plugins

TempMOTD, PlaceholderAPI, NametagEdit, SkinsRestorer, OldCombatMechanics, AsyncWorldEditInjector, LuckPerms, ClearLag, AdvancedBan, MessageAnnouncer, AsyncWorldEdit, OPSRegion, DeluxeMenus, LiteJoin, Vault, ProtocolSupport, ViaVersion, MyCommand, Chatty, WorldEdit, Essentials, AbstractCooldown, HeadDatabase, ProtocolLib, LibsDisguises, FiguresFix, Citizens, HeavySpleef, AdvancedAchievements, HolographicDisplays, AntiRelog, WorldGuard, ServerSigns, CommandNPC, EssentialsSpawn, TitleManager, PacketsBookFix, WGExtender, ReActions, AuthMe, ItemFixer, ItemJoin, LeaderHeads

Please explain your issue. How do you trigger it?
I'm logging in first time after restart server. Prefix on tab is existing. After text something in chat, prefix resets on tab and doesn't exist in message that i wrote.
If i execute /nte reload, prefix returns on tab, but after text something again or relogin it disappears.

Groups file written properly, i checked it many times. In permissions i set for each group only 1 permission. Other permissions i set false for each group.

Are there any errors in the console? Please use: https://pastebin.com
Debug output from console: https://pastebin.com/QAjJE6a0

+1 Running 1.16.1 Paper and I've noticed this issue as well.
I'll add that the issue is on a per-player basis. You may not see your tag but others still will (unless of course they get the problem as well)

EDIT : Installing and testing the latest dev build.

EDIT 2 : latest dev build (4.4.11) still doesn't seem to have this fixed.