Do you own a Powerflyer, by any chance? I have recently suffered some nasty HD read error problems and after much stress I found that the problem lay with the PIO setting and quality of cables used.
I have two HDs in my system, a Seagate40GB and a Maxtor40GB. The seagate works at PIO5 with no complaints, but the Maxtor complains bitterly at that level. I turned both drives down to PIO4, and replaced the IDE cable with a type recommended by a friend (ATA66 I think it was) and all has been fine since.
I use PFS... but like you was getting errors with FFS previously.
Hope this helps