Hmm. It should work.
1) Did you read everything on the MtkWinFlash page, including the note about nVidia IDE drivers (dunno if you have 'em, but just in case, I'll mention them)
2) Have you tried rebooting? (for the disabled drives)
3) Have you tried using IDE mode in MtkWinFlash?
4) Flashing in Windows can be quirky. DOS with MtkFlash is generally the best way to go, but most people get scared by the command line, which is why I recommended MtkWinFlash. You may wish to try this using MtkFlash in DOS. Look at digi's page for MtkFlash for details...
MtkWinFlash and MtkFlash pages: