1200 towers have this weird Voodoo curse on them I think. I tried *everything* (and I mean *everything*) with my Mediator 1200 tower and lost my rag and sold it in the end. Perhaps something to do with having a solid-as-a-rock 060 A4k desktop, maybe

I had everything from corrupt partitions to random gurus on boot, and when running software, and I tried everything in the book. I even booted the same hard drive on a 4000 and got non of the issues. I just don't think 1200s like being stuffed in a tower with all that extra hardware bolted on. I never *ever* have any issues with my 1200D/1230IV machine - it's as solid as my 4000D.
Anyway... Things to try...
I notice you are using a Powerflyer IDE controller. Have you tried removing it and using the internal IDE? I know removing the Powerflyer is a major op but it's the only way to eliminate it.
You could try using SFS filing system for the disk instead of FFS. I've found it way more reliable. However even this won't help you if you have a hardware issue.
Try pointing the IBrowse cache at RAM:, or even turn it off altogether. Even though they have reported them as fixed, some people still seem to think IBrowse has a tendency to damage the disk partition it's caching to. I don't know if it's true, and since 2.3 I've never had any issue with it myself, but my main machines all use SFS, which might be the key.
It does sound like a hardware problem to me though. Do you have anything on the clockport? I know that can screw with the IDE badly on some 1200 motherboards, but equally I've had no issues at all on others. They are on the same part of the bus.
Just out of curiosity also do you know your motherboard revision? It's not an evil v.1D4 is it?