I would DEFINITELY say that your motherboard is dead. I had a Chaintech VNF4 Ultra, and it was working fine until my power supply went. I moved to a new PSU and case, but the board would never respond after that (when I powered up, I got power, drives spun up, but I never got ANY video at all, and no beeps).
Nothing I did would get video out of it. I finally wound up trying another video card (still no video, etc), different RAM (same result), CPU (nothing different here) and different PSU's (still no go). Only when I replaced the motherboard did everything work again.
Part of the issue I had with the Chaintech board is that when it is dead, it acts like it is just a video-card issue, when it is in fact the motherboard that is the problem. It gives no error beeps, and aside from literally trying another 939 motherboard (not an easy extra to get if you are like me), you may never be able to tell what is wrong with it.
Before you RMA it, I would check that the ATX and 4-pin connectors are connected, and that you have no extra motherboard mounts shorting it from behind, but what you have sounds EXACTLY like what I had when my VNF4 died. Since you know the videocard works, and I presume that you can test the RAM, if you can verify the CPU is good too, then you can definitely say the board is dead, and send it back. Good luck.