Sorry about me leaving my previous issue and not checking back on it, I was a bit busy with some other stuff. I just reposted the information because the problem hasn't changed, but I made some edits below.

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 ((Im using Bukkit 1.2.5 R4-0 Build 2244 now)
Vanish v 3.10
Vanish Config:

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:
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
Server Save
Border Guard
Punishmental
Permissions
Creaturebox
SkylandsPlus
Lockette
ScheduledAnnouncer2
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.* , and I made myself OP so there is no reason permissons should be a problem. ((OP only gets vanish.op, which i have all permissions under that node)) I got rid of all of the Admin groups Inheritances so there is no conflicting permissions with negetive nodes.

I found out that if i am kicked from the server and log back in, all the permissions work. Its only if I hit the disconnect button myself and log back in.

Mbax, the last thig i saw was that you wanted my ENTIRE permissions config.
groups:
VIPTrusted4:
default: false
permissions:
- essentials.bcast
inheritance:
- default
- builder
- viptrusted3
- vipbuilder4
- g:essentials_builder
info:
prefix: '&5[VIP]&6[Trusted] '
build: true
suffix: ''
VIPTrusted5:
default: false
permissions:
- essentials.bcast
inheritance:
- default
- builder
- viptrusted4
- vipbuilder5
- g:essentials_builder
info:
prefix: '&b[VIP]&6[Trusted] '
build: true
suffix: ''
VIPTrusted2:
default: false
permissions:
- essentials.bcast
inheritance:
- default
- builder
- viptrusted1
- vipbuilder2
- g:essentials_builder
info:
prefix: '&9[VIP]&6[Trusted] '
build: true
suffix: ''
EliteMod:
default: false
permissions:
- ''
- vanish.
inheritance:
- g:essentials_admin
info:
prefix: '&f[Elite]&1[Mod] '
build: true
suffix: ''
VIPTrusted3:
default: false
permissions:
- essentials.bcast
inheritance:
- default
- builder
- viptrusted2
- vipbuilder3
- g:essentials_builder
info:
prefix: '&c[VIP]&6[Trusted] '
build: true
suffix: ''
ExtremeTrusted:
default: false
permissions:
- essentials.bcast
inheritance:
- default
- builder
- viptrusted5
- g:essentials_builder
info:
prefix: '&4[VIP]&6[Trusted] '
build: true
suffix: ''
VIPTrusted1:
default: false
permissions:
- essentials.bcast
inheritance:
- default
- builder
- trusted
- vipbuilder1
- g:essentials_builder
info:
prefix: '&2[VIP]&6[Trusted] '
build: true
suffix: ''
Admin:
default: false
permissions:
- ''
- vanish.
inheritance:
- g:essentials_admin
info:
prefix: '&8[Admin] '
build: true
suffix: ''
DonatorModerator1:
default: false
permissions:
- essentials.kick
- essentials.time
- essentials.time.set
- essentials.togglejail
- essentials.togglejail.offline
- essentials.unban
- essentials.weather
- groupmanager.manuadd
- groupmanager.manuaddp
- hawkeye.page
- hawkeye.search
- hawkeye.tool
inheritance:
- default
- builder
- trusted
- vipbuilder1
info:
prefix: '&2[$]&b[Moderator] '
build: true
suffix: ''
DonatorModerator3:
default: false
permissions:
- essentials.sudo
inheritance:
- builder
- trusted
- moderator1
- moderator2
- moderator3
- donatormoderator2
info:
prefix: '&2[$]&1[Moderator] '
build: true
suffix: ''
DonatorModerator2:
default: false
permissions:
- hawkeye.rollback
- hawkeye.search
- hawkeye.tool
inheritance:
- default
- builder
- trusted
- moderator1
- moderator2
- donatormoderator1
- g:bukkit_moderator
info:
prefix: '&2[$]&3[Moderator] '
build: true
suffix: ''
Builder:
default: false
permissions:
- -anticheat.xray
- -anticheat.fastheal
- -anticheat.fasteat
- -anticheat.forcefield
- -anticheat.fastplace
- -anticheat.noswing
- -anticheat.longreach
- -anticheat.spam
- -anticheat.spider
- -anticheat.zombe.noclip
- -anticheat.zombe.cheat
- -anticheat.itemspam
- anticheat.exempt
- bukkit.plugins
- creaturebox.breakspawner
- creaturebox.creature.cave_spider
- creaturebox.creature.cavespider
- creaturebox.creature.chicken
- creaturebox.creature.cow
- creaturebox.creature.pig
- creaturebox.creature.silverfish
- creaturebox.creature.skeleton
- creaturebox.creature.spider
- creaturebox.creature.zombie
- creaturebox.dropspawner
- creaturebox.placespawner
- essentials.delhome
- essentials.kick.notify
- essentials.plugin
- essentials.plugins
- essentials.sell
- essentials.sethome.multiple
- essentials.whois
inheritance:
- g:essentials_builder
- default
info:
prefix: '&2[Builder] '
build: true
suffix: ''
VIPBuilder4:
default: false
permissions:
- superpickaxe.use
inheritance:
- default
- vipbuilder3
- g:essentials_builder
info:
prefix: '&5[VIP]&2[Builder] '
build: true
suffix: ''
VIPBuilder5:
default: false
permissions:
- vanish.standard
inheritance:
- default
- builder
- vipbuilder4
- g:essentials_builder
info:
prefix: '&b[VIP]&2[Builder] '
build: true
suffix: ''
VIPBuilder2:
default: false
permissions:
- essentials.bigtree
- essentials.sethome.multiple.unlimited
- essentials.tp
inheritance:
- default
- builder
- vipbuilder1
- g:essentials_builder
info:
prefix: '&9[VIP]&2[Builder] '
build: true
suffix: ''
BannedBuilder:
default: false
permissions:
- essentials.spawn
inheritance:
- g:essentials_builder
- builder
info:
prefix: '&7[B]&2[Builder] '
build: true
suffix: ''
VIPBuilder3:
default: false
permissions:
- essentials.god
inheritance:
- default
- builder
- vipbuilder2
- g:essentials_builder
info:
prefix: '&c[VIP]&2[Builder] '
build: true
suffix: ''
VIPBuilder1:
default: false
permissions:
- essentials.chat.*
- essentials.chat.color
- essentials.chat.format
- essentials.chat.magic
- essentials.color.signs
- essentials.sethome.multiple.unlimited
- essentials.signs.color
- essentials.signs.format
- essentials.signs.magic
inheritance:
- default
- builder
- g:essentials_builder
info:
prefix: '&2[VIP]&2[Builder] '
build: true
suffix: ''
Default:
default: true
permissions:
- -bukkit.command.kill
inheritance:
- g:bukkit_default
- g:essentials_default
info:
prefix: '&7[Visitor] '
build: false
suffix: ''
Trusted:
default: false
permissions:
- essentials.broadcast
- essentials.kick
- essentials.sethome.multiple.vip
inheritance:
- default
- builder
- g:essentials_builder
info:
prefix: '&6[Trusted] '
build: true
suffix: ''
AdvancedBuilder:
default: false
permissions:
- essentials.sethome.multiple.vip
inheritance:
- g:essentials_builder
- builder
info:
prefix: '&a[++]&2[Builder] '
build: true
suffix: ''
ExtremeBuilder:
default: false
permissions:
- vanish.effects.toggle.smoke
- vanish.toggle.all
- vanish.vanish
inheritance:
- default
- builder
- vipbuilder5
- g:essentials_builder
info:
prefix: '&4[VIP]&2[Builder] '
build: true
suffix: ''
Moderator1:
default: false
permissions:
- essentials.kick
- essentials.time
- essentials.time.set
- essentials.togglejail
- essentials.togglejail.offline
- essentials.unban
- essentials.weather
- groupmanager.manuadd
- groupmanager.manuaddp
- hawkeye.page
- hawkeye.search
- hawkeye.tool
inheritance:
- default
- builder
info:
prefix: '&b[Moderator] '
build: true
suffix: ''
Moderator2:
default: false
permissions:
- hawkeye.rollback
inheritance:
- default
- builder
- trusted
- moderator1
- g:bukkit_moderator
info:
prefix: '&3[Moderator] '
build: true
suffix: ''
Moderator3:
default: false
permissions:
- essentials.sudo
inheritance:
- builder
- trusted
- moderator1
- moderator2
- moderator3
info:
prefix: '&1[Moderator] '
build: true
suffix: ''

Alright, let's do a test.

In your vanishnopacket config, set permtest to true.
Restart the server.

Log in and say these things in order:
/permtest vanish.fakeannounce
/vanish fakequit
(or vanish fakejoin if you joined vanished. whatever)

Let me know what those two say.

Now, log out, back in, see if /vanish fakequit (or fakejoin, whatever) doesn't work anymore. When it no longer works, do this
/permtest vanish.fakeannounce

And let me know what it says then. Could be different. This should help figure things out

Now join the game and

Hmm, so my internet's wonky and it derped the post up a bit. Ignore the last broken sentence.

Alright, give me a little bit to try, cause my server is actaully switching IPs and Host locations today (Which is what i was getting ready for last week), so i have to wait a few hours to transfer our data to the other location.

Restarted my server with permtest: true

(Accidentally pressed Ctrl+Enter to go down a line like in skype)
Restarted my server with Permtest: true
Logged on, and Silent join worked. did /permtest vanish.fakeannounce and it said You have vanish.fakeannounce. I did /vanish fakequit and it worked. I have a slight issue though.... when i logged out and back in, it said "Failed to verify username" and it did this on every server i tried. It wont let me back in the server, so i cant test it again.

@MichiganMinecraftServer Minecraft was down. At this time the servers are back online.

Alright, test it out again now that hte servers are up :)

Alright I tested it again after the restart. I logged on and it said that i had vanish.fakeannounce just like my previous comment. I logged out and back in and type /permtest vanish.fakeannounce it said You do not have vanish.fakeannounce.

I did find something else out though. If I get kicked, like if I spam and get auto-kicked, when I log back in I will join vanished and have the permissions. Same with all of the other people who have vanish permissions.

Alright, this confirms it's a problem with your permissions plugin. The /permtest command directly queries the Bukkit permissions API, so this means your permissions plugin is broken.

I've seen a lot of people have trouble with GM lately, and I've been suggesting they use either bPermissions or Privileges as a replacement (Don't move to PEX/PermissionsEx, that's like intentionally lighting your server on fire!)

Alright, thanks for the help.... im not looking foward to redoing all these permissions

I hate redoing permissions too, but the few minutes spent doing it is worth it in the long run :)

@mbax But WHYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY