I had the exact same problem with the card reader in my A1500, where I could get HDToolBox to recognize both a CF and SD card, but not at the same time. After an whole evening of LUNacy, I finally gave up and tried HDInstTools instead, which worked like a charm. The reason for this is because HDInstTools has a Last Lun option, and something similar seems to be missing in WB3.1 HDToolBox.
Now I'm able to use three cards at the same time if I want to (PCMCIA-CF, CF & SD).