i really dont have much experience with outside box audiocards (usb or firewire) but i know they are doing whatever a pci slot audiocard does. of course, quality and features vary depending on the models, etc.
i am sure there are members here that have alot of experience with that, they can post. definitely, there is a limitation of usb1.1 old cards, but with usb 2.0, they are suppose to replace successfuly the internal audiocards.
anyway, regarding your problems with recording stereo, i can think of
1. bad cable
2. bad jack connection both/either on cable and soundcard
3. bad settings in the audiocard mixer
4. bad driver or driver's settings
5. bad settings on recording software

but i am sure you checked all of these... so i am out of ideas.