or the master/slave jumpers are wrong.
I've found that if you don't use a slave, jumpers aren't usually required, but that's with IDE drives. Using a CF card as a hard disk is totally new to me so your results may vary.
Odd boot problems can occur if an IDE cable is backwards, incorrect
I can attest to this. Really old IDE cables don't have that little notch to tell which way is up. Hook up a hard drive backwards and you get a disk failure error. Hook up a CD-ROM drive backwards and get a lot of BIOS error beeps with no output to the screen.
Whenever I take apart a system or system component that I'm not familiar with, I try to draw a diagram of how it goes back together. This may help prevent this problem in the future.