I spent way too much time over the last few days chasing bugs which turned out to have nothing to do with Linux.
I bought a SATA controller which arrived just before the weekend. It seems there is a fundamental flaw with the Silicon Image 3114 chips. Or to be more precise, with the firmware on some of the boards using this chip.

This thread is a summary of all manner of problems with it, but in short, it corrupts data past a certain block number. This took a lot of tracking down. (And badblocks takes forever to run when in destructive mode).

There is mention in that thread that a firmware update fixes the problem. Unfortunately, the DOS based flasher program seems completely unable to even write to my card.

I guess I’ll only use this controller for smaller disks, unless someone comes up with a workaround.