I have added these registry tweaks to my list..

I have added some new tweaks to my Tweaks.reg file in my unattended XP CD, they seem to be causing me some issues, my computer now takes almost 3 years to shutdown or restart.

The entries in the code box below are the new entries, I have tried the installation without these and shutting down or restarting is fine.

; Remove Print From TXT Files

[-HKEY_CLASSES_ROOT\txtfile\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From Images

[-HKEY_CLASSES_ROOT\SystemFileAssociations\image\shell\print]
[-HKEY_CLASSES_ROOT\SystemFileAssociations\text\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From REG Files

[-HKEY_CLASSES_ROOT\regfile\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From CMD Files

[-HKEY_CLASSES_ROOT\cmdfile\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From Batch Files

[-HKEY_CLASSES_ROOT\batfile\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------


; Remove Print From INI Files

[-HKEY_CLASSES_ROOT\inifile\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From INF Files

[-HKEY_CLASSES_ROOT\inffile\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From PHP Files (Change AppName, To Name Of Default App For File Type)

[-HKEY_CLASSES_ROOT\AppName.php\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From PDF Files (Change AppName, To Name Of Default App For File Type)

[-HKEY_CLASSES_ROOT\AppName.Document\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From Word Docs

[-HKEY_CLASSES_ROOT\Word.Document.8\shell\Print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Print From PowerPoint Docs

[-HKEY_CLASSES_ROOT\PowerPoint.Show.8\shell\Print
;--------------------------------------------------------------------------------------------------------------------------------

; Remove Record From Wave Files

[-HKEY_LOCAL_MACHINE\SOFTWARE\Classes\SoundRec\shell\record]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove "Print" option from the context menu for image & text files

[-HKEY_CLASSES_ROOT\SystemFileAssociations\image\shell\print]
[-HKEY_CLASSES_ROOT\SystemFileAssociations\text\shell\print]
;--------------------------------------------------------------------------------------------------------------------------------

; Remove the Map and Disconnect Network Drive Options

[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Policies\Explorer]
"NoNetConnectDisconnect"=dword:00000001
;--------------------------------------------------------------------------------------------------------------------------------
; Faster reboot time

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon]
"EnableQuickReboot"="1"
;--------------------------------------------------------------------------------------------------------------------------------

; Disables Backup System Files with Successful Boot

[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\CurrentVersion\Winlogon]
"ReportBootOk"="0"
;--------------------------------------------------------------------------------------------------------------------------------

;Prevents Windows Messenger from being updated

[HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Microsoft\Messenger\Client]
"PreventAutoUpdate"=dword:00000001
"PreventBackgroundDownload"=dword:00000001

; Disable Default Hidden Shares - This keeps Windows from creating the  Admin$, C$, etc. shares (which are security holes) automatically on start-up.

[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\LanmanServer\parameters]
"AutoShareWks"=dword:00000000

[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\LanmanServer\Parameters]
"AutoShareServer"=dword:00000000
;--------------------------------------------------------------------------------------------------------------------------------
; Fix for DSO Exploit that Spybot complains about

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Internet Settings\Zones\0]
"1004"=dword:00000003
;--------------------------------------------------------------------------------------------------------------------------------

; Speed up shutdown

[HKEY_CURRENT_USER\Control Panel\Desktop]
"AutoEndTasks"="1"
"HungAppTimeout"="100"
"WaitToKillAppTimeout"="1000"
;--------------------------------------------------------------------------------------------------------------------------------

; Force DLL To Unload From Memory

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\AlwaysUnloadDLL]
@="1"
;--------------------------------------------------------------------------------------------------------------------------------

; Speeds up copying/moving of zip files (disable windows built in zip functionality)

[-HKEY_CLASSES_ROOT\.zip\CompressedFolder]

[-HKEY_CLASSES_ROOT\CLSID\{E88DCCE0-B7B3-11d1-A9F0-00AA0060FA31}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Classes\CompressedFolder]
;--------------------------------------------------------------------------------------------------------------------------------

; Multiple Explorer Processes meaning its more stable

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer]
"DesktopProcess"=dword:00000001
;-------------------------------------------------------------------------------------------------------------------------------

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\SharedDLLs]


"C:\\Program Files\\Common Files\\Adobe\\Shell\\psicon.dll"=dword:00000001


[HKEY_CLASSES_ROOT\.psd\ShellEx]


[HKEY_CLASSES_ROOT\.psd\ShellEx\{BB2E617C-0920-11d1-9A0B-00C04FC2D6C1}]


@="{0B6DC6EE-C4FD-11d1-819A-00C04FB69B4D}"


[HKEY_CLASSES_ROOT\CLSID\{0B6DC6EE-C4FD-11d1-819A-00C04FB69B4D}]


@="Photoshop Icon Handler"


[HKEY_CLASSES_ROOT\CLSID\{0B6DC6EE-C4FD-11d1-819A-00C04FB69B4D}\InProcServer32]


@="C:\\Program Files\\Common Files\\Adobe\\Shell\\psicon.dll"


"ThreadingModel"="Apartment"

;-----
;-----  Speed Up browsing remote computers (Your Network)
;-----
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\RemoteComputer\NameSpace\{D6277990-4C6A-11CF-8D87-00AA0060F5BF}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\RemoteComputer\NameSpace\{2227A280-3AEA-1069-A2DE-08002B30309D}]

;-----
;-----  allows boot files to be placed optimally on the hard-drive for faster boots.
;-----
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Dfrg\BootOptimizeFunction]
"Enable"="Y"

;-----
;-----  Prevent "Start" menu popping up on windows first boot:
;-----
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Advanced]
"StartMenuInit"=dword:00000002
"StartButtonBalloonTip"=dword:00000002

Here is my main Tweak.reg file, the above tweaks have been removed. Tweaks.reg

EDIT:

I have been messing around and I changed the entry below from 5000 to 1000, this matches it up with the "WaitToKillAppTimeout" tweak, it seems now my computer shutdown instantly.. well it should no doubt. I am now adding the all the new tweaks back in + this "WaitToKillServiceTimeout" tweak to see if it makes any changes.

[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control]
"WaitToKillServiceTimeout"="1000"