Interesting. FYI, my 3000 with latest SCSI chip boots to the CF card reader without issue. I did need to enable LUNs to get it to recognize the CF card slot.
Also, HDToolBox did error out trying to partition the card when in the CF card slot. I used the PCMCIA adapter just to partition, format, and install the OS. Once I did that I moved the CF card directly to the CF card slot and it has worked fine since.