This issue has been going on since my server updated to CB 4-0. I updated just about every plugin I could (Including vanish) and this problem continues. The plugin works completely fine just how it used to right after I restart the server, until I log out and back in. Then NOTHING but the no-visibility part works. I am OP'd and have all of the permissions that I should have. Whenever i do /v t NoInteract it says "You can't toggle that!", and /v fakequit f says "[Vanish] Access Denied". Everything works PERFECTLY right after a restart. Toggles are good, effects, all the permissions for my Donator groups work (They can't even vanish upon relog), everything until I Disconnect from my server, and re-connect.

Stats: Bukkit 1.2.5 R4-0, build #2222
Vanish v 3.10
Vanish Config

VanishNoPacket

A fine choice of invisibility for the discerning server administrator.

http://www.kitteh.org

fakeannounce:
automaticforsilentjoin: false
join: '%p joined the game.'
quit: '%p left the game.'
hooks:
essentials: true
dynmap: false
JSONAPI: false
spoutcraft: false
checkupdates: true
permissionsupdates:
checkonworldchange: false
effects:
lightning:
count: 1
permtest: false
debug: false
configVersionDoNotTouch:
SeriouslyThisWillEraseYourConfig: 4

All out plugins are up to date that need to be, the plugins I thought may be important in this ill put (Up to Date) to eliminate confusion. PLugins with this "~" means i added them when I updated to CB 4-0 (They are new)

Plugins:
TimeTheEnchanter
GroupManager (Up to Date, 2.9.1)
Minequery (Up to Date)
EnderCrystalizer
Spout Plugin (Up to date, Build 1216)
Signlift
Multiverse (Up to Date)
Mobile Admin
~ColourFireworks
Server Save
Border Guard
Punishmental
Permissions
Creaturebox
SkylandsPlus
Lockette
~ScheduledAnnouncer2
~WeatherMan
MobDisguise
Superpickaxe
World Guard
DynMap (Not working because of TCP port confliction,)
Honeypot
HawkEye
World Edit
Essentials-Spawn-Protect-Chat (Up to date, Pre 2.9.2.4 for R4-0)
And of course, VanishNoPacket, up to date, version 3.10

I have reinstalled these plugins about 4 times, messed with vanish's configs, tested out Vanish without plugins being installed, and looked and looked at changelogs to find any thing that could be messing up vanish (Mostly permissions based changes). I did notice ESSENTIALS saying something about a /vanish command but i did not test out my server without essentials because I absolutely NEED that plugin 24/7.

If anyone is willing too, i can show people first hand my issue. Connect to MMS, IP: 72.9.145.202:25583 and ask for Spec. If I'm not on, someone should be able to give you my skype name, and if not, i don't know what to say, try again later.

I am soo frustrated right now and I am loosing players because of all these restarts I need to do. I know of a server with similar plugins like Essentials and Hawkeye who had this SAME problem, and It's now fixed now so I KNOW there is a way to fix this and I'm pulling out my hair trying to find it! Please by all means help! I don't know whats wrong!

Permissions: I'm using Group Manager and I have given the Admin group vanish.* , vanish.standard, and a whole bunch other nodes, and I made myself OP so there is no reason permissons should be a problem. I got rid of all of the Admin groups Inheritances so there is no conflicting permissions with negetive nodes.

If it's suddenly saying you can't toggle things, then it means you no longer have the toggle permission node granted. It's a problem with your permissions plugin. :/

Op only gets a handful of nodes in this plugin. Node lists here: http://vanishnopacket.github.com/permissions/

I know it sounds weird, but if you suddenly don't have silent login then the permission node isn't being applied to you by your permissions plugin. You should ask the GM folks for help.

It doesn't make any sense that the Permissions plugin would be the problem. It works PERFECTLY right after i restart. Everyone has the permissions, my toggles work fine etc. If i disconnect and reconnect, I dont have silent loggin, and i can't toggle anything. The only thing i can do is /vanish, and the NoInteract, no chat, no agro all dont work. To make it less likely, I'm OP'd so I can edit groups i don't inherit and change my own group with getting "You can not edit a players group with the same permissions as you" from Group Manager. I'm about to whitelist the server so I can test without GM, and me having OP (Which if I'm not mistaken, you get every permission node with OP by default).

Sigh... So I reinstalled group manager and manually added vanish., vanish.toggle, vanish.op and vanish.standard. I restarted the server, and it wont even work right after a restart anymore. I type /help vanish, and this should give me a list of all permissions i have access to for Vanish, but I only have /Vanish and like the vanish help command, no toggles or anything else. My next thing to do is try an earlier version of bukkit, like R-3 or something

Paste your ENTIRE permissions config.