This is an odd sort of problem and I guess I don't really expect any solutions.
I have two old Maxtor 51536U3 that I use as "town ponies" on my test system. Usually they resided on an old FastTrak66 controller. I was experimenting with hdparm, which may have been the crux of the problem. I needed to use them for a new project this week and I couldn't get the system to boot with either of them connected. DOS 5.0 (!) booted just fine, of course. I managed to get knoppix running and disabled all the hdparm stuff I did, but that didn't help. I finally had to load Maxtor's PowerMax software under dos and do a low level format to get them straightened out. Before I ran the Maxtor stuff, the linux installer (Sarge and Etch) would fail at random points during the initial boot process.
Like I said, strange stuff, but at least it's fixed. Wish I had at least some idea of what happened. I'm kind of suspicious it's related to when I converted the FastTrak66 back to an Ultra66 for awhile.
Hell this is so confuse I probably shouldn't even press the post button.