Your problem got nothing on mine, I get a new harddrive so I put it in as the slave and go to partition it, as soon as I type In Fdisk it decides to lose command.com and won't accept the C:windows one.
SO about an hour later and a few startup disk later its partioned and formatted. I then go to windows ME and use it to perform a fresh install of XP on the D: drive which work fine. Then I decide that it would be better to switch the D: drive to the master, so I do so. I restart the computer to find it keeps asking for a system disk and won't start windows.
SO i figure I'll just reset the drives to how it was when it worked, which then wouldn't work!
In the end I had to put the drives so the new one was the c: drive, format it, install windows 98 on it then uprgade to win XP to get it to work.
I now know that harddrives have something against me!