Some interesting developments!
I installed a fresh copy of Windows, and all the VIA and nVidia and so on drivers. At some point during all this (a period of relatively heavy disk IO), the computer seemed to crash and I rebooted it. It then worked fine for a while, but during my perfmon testing it seemed to do the same thing. This time I left it for a while and it did eventually wake up again, so I'm guessing the controller is a bit fubared. Perfmon did indeed show several dips down to or very close to 0 during the write operation, with peaks up to 48 MB/sec, which is pretty respectable. So, time to replace the brand-new controller I guess.
Now, do you think this is just my one particular controller card and a simple return would fix the problem, or is it more likely a problem with the whole range? It's an Innovision EIO SATA controller: http:// www.ivmm.com/eio/products/index.htm
Would it be a safer bet to go for the Adaptec controller of the same variety? How reliable are they?