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I am unable to finish booting a hard drive I have Windows 98SE installed on (a single partition.) I had had some unexpected trouble and needed to replace the registry and some system files. I've used sys C: and a copy of user.dat and system.dat from another HDD I have on the same computer which has a little more than Win98SE installed on it.
My repaired drive will not boot normally, ie: configured as HD000 in my bios and in the master position on IDE cable. However, if I make it a slave on my other drive's cable and configure my bios to boot HD001 it DOES boot normally. I thought perhaps there was a problem with the master boot record, so I tried both installing a bootloader and using fdisk /mbr to reset it to WIN98 standard- neither of which worked. Where would the difference/ dependancy arise if my bios is simply booting from the slave and not the master? The problem shouldn't be the MBR, nor the boot code of the partition windows is on, nor the windows registry as far as I can see.

If it's a Western Digital drive and alone on a channel, It has to be plugged as 'single', not master or slave.

Both drives are the same, Maxtor 40Gig. The jumpers are set to cable select, which has worked fine for switching between master and slave configs for me in the past with these drives. Thnx though.

You replaced the registry with a copy from your D: drive. All of the registry entries point to D:\Windows, not C:\Windows. Thus, it won't boot when you connect it as your C: (Primary Master) drive.
You're kinda screwed now, unless you have a backup of your original registry. You could TRY booting with a bootdisk & typing:
Scanreg /fix (ENTER)
or
Scanreg /restore (ENTER)
I'm not sure if either will work, but it might be worth a try.
The only sure-fire solution would be to reinstall Windows on top of itself. (NO format.) You shouldn't lose any data or settings, though backing up important data is NEVER a BAD idea.
HTH
Dave

Never take a copy of user.dat and system.dat from another machine.
No two machines software arrangements are anywhere near alike, despite using the same OS. Your registry should always match the file structure and program installations as closely as is possible.
For this reason I would even advocate running scanreg /fix on a machine before resorting to scanreg /restore (which by definition creates a mis-match).

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