I have one of these card readers (not your model), What I have found is that the usb-storage module needs to be loaded for the device to be detected.
What version/distro of linux do you have?
The problem, which you may have already found, is that often just the first port gets recognized correctly. In my case, it is the compact flash port, which happens to be the one that I need.
Look at dmesg and see if the ports are detected.
You need to have the flash card inserted at boot time, in most cases, for the card's port to be detected,