While those programs are nice for beginners, as you just found out it's always better to just do things yourself so you know exactly what's going on.

If you're famililar with vi, open a terminal and do

sudo vi /Library/Preferences/SystemConfiguration/com.apple.Boot.plist

edit and save. If you have no idea what vi is, then just use Finder to navigate to that folder and drag the file onto your desktop, open it, make your edits and save, then drag it back to that folder. It should ask you to authenticate, and whether to replace or not.

Now go read up on vi, since it's a standard on every *nix.

http://www.macdevcenter.com/pub/a/ma.../vi_intro.html

On a side note, NVkush shouldn't require you to boot with -f everytime, if it does you might want to try NVInject and see if that works better for you.