Messages not showing up for ops/admin

We are having this anoying problem where any server or plugin messages usually do not show up for anyone who is an op. For example, the [Server] messages, dynmap messages, [Broadcast] Messages, ext. The weirdest part is that sometimes they do work, but they useally do not. Any help with this is much appreciated.

Plugins:
Plugins: LagMeter, WorldGuard, MultiInv, MinecraftViewer, Rakamak, CFBanner, Essentials, Spout, NoCheat, Minequery, Permissions, VanishNoPickup, EssentialsSpawn, EssentialsGeoIP, WorldEdit, Multiverse-Core, MCTelnet, chatclear, Locker, EssentialsChat, dynmap, WorldBorder, MobArena, LogBlock

 

• Make sure that you are properly updated. (craftBukkit and plugins)
• Make sure that it is not you server's problem by running a vanilla (Not craftBukkit) server on you computer. If that doesn't fix the problem, we can not help you.
• You might need a newer permissions system. (Isn't "permissions" the old one)