I think it has to do with the transfer modes which the card supports. On some machines, a card in an adapter will give errors (NetBSD kernel messages) because higher speed modes won't work, and the speed is then lowered in steps until it starts working with one of the PIO modes.
I have three different kinds of adapters, and only one CF card larger than two gigs which works in any of them, so I can't say for certain what will and what won't work, but all of the cards I've tried which are two gigs or smaller (all the way down to an 8 meg card!) work fine for some reason. I have them in two different Amigas (on the motherboard IDE), on a Motorola Starmax, a SCSI-IDE adapter, and a typical x86 motherboard. They're not fast, but they work.
Have you tried any smallish cards?