Well you can use ERD Commander (like a Linux Live CD) and use the registry editor within to remove entries from MSCONFIG. If you need to change options that are within the tabs on MSCONFIG
I would bet there is a way to do it using the correct path in the registry.
ERD Commander: http://www.fullandfree.info/software...ommander-2005/
If you are not familiar you need to burn the image of ERD Commander to a CD and boot your PC from it. It will bring you to a Windows environment with troubleshooting tools available in the start menu.
To Remove Entries:
The enabled (checked) items can be present in any of the following registry entries:
In the right window pane, the value named Run (REG_SZ Run can be set to launch an application at startup e.g. "notepad.exe") This is not present by default, unless you've added the value manually.
Expand the "Location" column in the Startup tab to determine the exact location of the command.
The disabled (unchecked) entries are present in any of the following locations:
Quoted from: http://www.zappersoftware.com/Help/how-to-msconfig.html