I was able to figure things out, at last!
I had two issues:
- my cable was unkeyed (always get keyed cables ). Once I hooked it up right, it worked a lot better.
- the Alix only uses a single PATA channel, so anything connected to the connector has to be in slave mode, at least if you're still using a CF card in the on-board slot. (It might be different if you're not, but I didn't try this combination.)