Do you have a smaller CF card that you could try? I have had problems getting my SEs and SE/30 to recognize, let alone read or write to, certain large hard drives, especially external ones. For example, I have a 2GB Quantum drive in an external case that worked great with the SE/30. I connected it to one of my SEs to transfer some things, and it immediately asked me to format it...skipped that, ran Disk First Aid, works fine, BUT not on the SE/30 anymore. When I connect it to that, it will either not boot at all, or it will do a partial boot and the system folder has to be re-blessed to boot normally again.

Smaller, Apple ROM drives work fine, in contrast.