Have a look around this area in the Registry.
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig
MSConfig Cleanup
Removing a Program from Startup in xP
thread779-631159
"If you want to do this manually, Kelly Theriot wrote:
Start, Run, Regedit
For items that were in the Start menu, Programs, Startup folder:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig\startupfolder
You'll find a subkey for each disabled item.
For items loaded from the Registry:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\MSConfig\startupreg
You'll find a subkey for each disabled item.
Another Option:
Start/Run/Regedit
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run.
In the right pane, delete the value for MSConfig.
Alternatively, you can use a small VB Script file to do this for you as well. Copy the following three lines to a Notepad file and save as No_MSCONFIG.VBS
On Error Resume Next
Set WshShell = WScript.CreateObject("WScript.Shell")
WshShell.RegDelete "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run\MSConfig".
After running MSConfig, run the VBS file and this entry will be removed automatically."
Thanks to B. Castner for the above quote.