Msconfig will identify any "invalid" entry but it will not delete it
(permanently)!
Also, boot.ini is "read only". You didn't mention that.

Scroll down to #20
http://www.michaelstevenstech.com/xpfaq.html

"Trax" wrote:

> RiderDude <RiderDude@discussions.microsoft.com> wrote:
>
> |>one of my dumb kids infested my dell dimension 2400 with everyspyware program
> |>known to man (and a few unknown ones). i tried washing them out, and
> |>scrubbing them out, but the stains were still there. i ended up doing a clean
> |>install of XP from the disks which i miracuously found in the attic. deleted
> |>all partitions and built a single new NTFS partition and nestled XP snugly
> |>therein. problem is, now when i boot, BIOS thinks there are 2 OSs on the disk
> |>and asks me to choose the one i want to boot from. one works (i'm assuming
> |>this is the newly installed version), the other doesnt (i'm assuming it's a
> |>ghost of the old OS rattling around like Jacob Marley). how can i get rid of
> |>Marley's ghost?
>
> You didn't do a clean install, the boot.ini has both systems listed
> now.
> Start | Run | MSCONFIG <enter>
> goto boot.ini and click on - check boot paths.
>
> Or edit the extra OS out of C:\boot.ini
>
> --
> http://blueballfixed.ytmnd.com/
>