Use FDISK to see if the 40GB drive in the PRIMARY IDE and MASTER has an ACTIVE partition. Some MALWARE loves to unset that and cause issues.
You do have a backup of what you can't lose?
I have an old, Compaq computer with 2 HDs, a 6 gigabyte one with WIN 98 (on secondary master) and a 40 GB one partitioned 5 ways, with Win 98 SE (on primary master). I installed the 40 GB drive a couple of years back and it has been working fine. Then all of a sudden a week or two ago, the computer booted to win 98 (aka the 6 gig drive). However, when i look at My Computer, 4 of the 5 partitions for the 40 GB drive exist with the one containing win 98 SE excluded. Also, if this is important or not, a few times the computer has booted up with just the 6 gig drive displayed in My Computer and about half the time I can see the CD-rom. Thank you in advance for any help/suggestions.