After booting from a system or boot disk a "RamDrive" or virtual drive is created - usually in the "D" drive spot....all other drives installed above "C" will be moved up one spot to accomodate the new Virtual RamDrive now located @ "D". IE: if yournormal "D" drive was your CDROM it will now be "E" (only until the system is re-booted without using the boot disk).
The way to check is: after you get to the A:\ prompt while booting w/ a system or boot disk, type DIR (should look like "A:\DIR" should be the dir of the floppy in the drive, or "C:\DIR" should see the dir of the HDD or "D:\DIR" should see the dir of the new Virtual RamDrive (which are the actual highly expanded and now useable files that are located on the start-up disk) or "E:\DIR" should be the dir of a CDROM if you have a data CD in the drive).
After you boot using a boot disk, try going to A:\ or D:\, then try this... type "A:\ SYS C:\" This should transfer the system files from A:\ or D:\ to C:\, it will tell you that the files were actually & sucessfully transferred to C:\.
Remove the boot disk and reboot the computer by hitting the reset button, upon re-boot the Virtual RamDrive will be gone and all drives will be back in the normal lettered position.It could be that the CMOS isn't set right to recognize the hard drive, set @ auto or try to auto find the drive. Check the drive spec's. against what the CMOS finds...IE: Sectors, Heads, Cyl'S. Normal, Large, LBA, ETC. You could write down the drivespec's. seen in CMOS of the working system (2nd. system you put the drive in and the drive worked). Set the first system's CMOS to the same HDD settings. That would be a good start.