1854 windows98SE problem

I have an 1854 with Windows98 SE. My primary hard drive was 10 g, my
secondary was 40G, and I had a 9G scsi as the third physical drive. All
worked well, but I noted the primary drive had a large number of bad
sectors. This weekend, all of a sudden I could not access any but the C
drive (right click on start and select explore and it freezes). I also
had troubles running any programs that had to access other than the C
drive. I finally tried to reinstall windows, but it reported that there
was some problem with the drive and would not install. I broke down and
had an 80 G primary drive installed (I also had removed the 40 G
secondary drive trying to eliminate possibilities). Now I have the same
problems with the new drive. When I tried to reinstall windows it
reported that there was some problem with the drive and suggested I run
scandisc; I ran it and the drive is fine. What's puzzling to me is that
some programs can see the other drives, although windows apparently
cannot. FSAV, for example, is now running a manual scan of both
drives. I think my antivirus is pretty good, but am running another
scan now.

Does this sound like a hardware or software problem? I'm at a loss what
to do next.
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