I had the same issues as you. I'm using one of those little Hacom systems for my pfSense install, and I initially wanted to use a super-fast 1GB CF card to install it, but had all those DMA timeouts. Via Google searches I saw lots of suggestions to disable UDMA and to set the access mode of the port (for the Hacom using CF it's Master on the Secondary controller) to CHS. That didn't help, but I tried a 256MB card and that worked. However I didn't want to use a small 256MB card so I went to some stores and bought the cheapest 1GB CF cards I could buy. Sure enough, some cheap 1GB CF card that was on sale for $12 worked immediately. I even bought another one to have as a backup.
I don't know if this will help or not, but you may want to first bring down the speed of the interface you're connecting the CF card to down to non-UDMA. Second, try some other cards. I suspect that the nice high-speed CF cards have less of a chance of working than the el-cheapo CF cards. Just a guess.