Double checking your setup, I'm assuming this is a IDE based system.
Primary Master is the CF card
and you plugging the mechanical HDD into either Primary Slave or either secondary master or secondary slave
assuming you also have a Optical drive plugged in somewhere?
First check is to make sure BIOS picks up the drive?
if not check the drives jumper and you can also try moving it to the other IDE channel.
if Bios does show the the drive can dos access the drive? (Shift F8 as soon as you see starting Win98 in text mode)
If you can then we know its a windows issue, but I doubt this
More likely dos wont be able to access either in which case run fdisk and see if it recognises any partitions, if it doent understand the partition scheme then windows won't either.
If thats the case the question is what was used to create the partition and on file system Fat/NTFS, etc?