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Are you missing "msconfig.exe" in Win2k?
Copy the "msconfig.exe" from your Win98 folder, or extract it from a Win98 CD, into your X:WINNT folder. Then, in Win2000, click on "run" and enter msconfig before pressing enter. This can be used on dual boot systems to select or edit the default boot sequence in the "boot.ini."
I used this method to edit my "boot.ini," removing the command for Win2000, thereby making "windows" the default command. I also used it after booting into Win98, shutting down restarting in DOS, and using the "deltree" command to delete the WINNT folder. I used it again on another system, using the "deltree" command to delete the Windows folder, thus having only one operating system installed and set as default.