alright, so let's go over this-
Your trying to connect the SPDIF out header on the motherboard (I assume from onboard sound?) to the video card (which I also guess uses the audio, and it's own video to create a HDMI signal) You don't list a video card... are you using the on-board video as well?
Is this your motherboard
here? as you said it labels the SPDIF out 2 connector but not the actual pinouts.
This thread
here might be helpful; post #6 lists some pinout info, but it's five, not 3 pins. however- the two pins on the right in the image are NC (not connected) and IN, neither of which would be used for the graphics card connection. If you can identify pin 1 on the header, (usually indicated with a small triangle on that side, or other unique marking) then you should be able to identify VCC, OUT and GND, of which you want OUT and GND (if I understand your dilemma) which would be pin 2 and 3. I can't really make out much from the image, myself, though. most connectors of this sort have a notch in the plug and the header to make sure you plug it in the right way. on the header, the notch can usually be thought of as the top, and the pins are left to right.