So is the d: drive part of an extended partition which also includes logical linux drives too? If so, this may be causing a problem (you may need to backup the d: drive then remove & recreate the extended partition with just a fat32 logical drive - no linux - in it. Then copy data back & try again). have you just tried booting using the ghost boot disk? If so, try a normal win98 boot floppy to see if you can see d: drive from there.
Though, reading your post again - you say the POST sees the d: drive - so is it a separate physical drive? And if so, how is it partitioned?