I ran into the ghost hard drive problem myself; C: and D: were identical copies of my IDE drive. I FDISK'd the drive back to square one on another machine and reinstalled DOS on it with the DOC utilities and reformatted the DOC as well. The problem disappeared.
Not sure what caused it. If you follow the directions as laid out in other posts you should be ok though.
ie, to use the IDE drive, turn off the primary IDE controller in your BIOS and also set the boot option to "D,SCSI", and set the drive itself to slave. Your DOC *should* show up as D: at this point, but if you've used the dformat command with /first, you might screw it up. You should be able to stick the doc123.exb image on the DOC, copy DOS to it, and sys it. You should never have to use the /first option or the /floppy option.