When you formatted the drive, it sounds like you SYS'd it as well.
That will usually give you a Win98 logo screen and it will definitely look
for COMMAND.COM
Which in turn also suggests that the Win98 partition is marked as active.

You can change the active partition with pqmagic.
Then yes, I'd try FIXBOOT and/or FIXMBR

"Tim Haynes" <timhaynes@alumni.NO.SPAM.PLEASE.uwaterloo.ca> wrote in message
news:dnpgke$vjt$1@rumours.uwaterloo.ca...
> Okay, here's a weird one. I think the solution may be simple, but want to
> see what others think.
>
> A friend has a very old 6GB drive that I'm replacing with a new 80GB
> drive. The 6GB drive has been randomly failing. It will often boot into
> safe mode but then blue screen after a few minutes.
>
> The old 6GB drive previously had Win98 on it, and had been upgraded to
> WinXP Pro.
>
> I cloned the old HD onto the new HD, and tried booting the new HD.
>
> Strangely, it tries to boot into Win98 (even shows the Win98 boot graphic
> for about 2 seconds!) and then immediately dies horribly, asking where
> COMMAND.COM is.
>
> Now, the old drive never tried to boot into Win98. It always booted into
> WinXP.
>
> Why would the new (cloned) drive try to boot into Win98?
>
> Here is how I cloned it:
>
> 1. Old drive is the slave (D and the new drive is the master (C.
>
> 2. Used Partition Magic to copy the primary (and only) partition from the
> old drive to the new drive. It died about halway along because of too
> many errors (the old drive is failing, after all)
>
> 3. Used Partition Magic to define and format a FAT32 partition on the new
> drive. (The old drive had FAT32, and I knew I'd have to use DOS to copy
> the old drive's filesystem onto the new drive, crossing my fingers that
> only useless files would be unable to copy).
>
> 4. Used a WinME boot disk and FDISK to make the new drive's partition the
> primary active partition.
>
> 5. Used the same WinME boot disk and LCOPY.EXE to copy the filesystem from
> the old drive to the new drive. A few files failed, but I wasn't watching
> to see which ones.
>
> 4. Set the BIOS to boot the new master drive.
>
> 5. The new drive starts booting into Win98, then crashes, asking for
> COMMAND.COM.
>
> The boot.ini looks fine to me. It's identical between the old drive and
> the new drive, and the new drive attempts to boot WinXP just fine.
>
> I tried to start a Repair install of WinXP, but the WinXP setup CD doesn't
> give me the option. It seems to think that whatever is in C:\WINDOWS is
> useless and that it would be okay to completely overwrite it (losing all
> settings, users, user files, etc... which we definitely DON'T want to
> do!).
>
> Any ideas on what I can do to make the new drive boot into WinXP?
>
> Thanks
> Tim