Many of my tests yesterday gave me zeros on the status register. I played with it for a while with no avail, but I decided to treat the motherboard as if the expansion ports support hot plugging (they shouldn't). To my surprise not only did the computer not crash, but the CF card actually started working! Almost.
The card gave me an error code: 0x10, aka Sector ID not found. As of yet I haven't found out exactly where this error comes from, but I think it means that the sector doesn't exist. I set the sector to zero, but I am currently using a crappy test driver that is probably the issue. But, I'm talking to it!
You will notice that usually the number (the status, in hex) is 51, bit one being set meaning an error occurred. when I remove the CF card it becomes 50 once, indicating no error. This means my driver code is broken.
I am going to play with someone else's driver, will post another log.