I had this exact same problem, but for a totally different reason.
First, my card was running fine, but I have an extremely quiet system so the video card was dominating the noise. So I tried to install an Accelero S1 Rev. 2 on it to quiet the card a little. The Accelero fit OK, however, when I tried to start the system, I first recevied an error about the power plugs not being inserted. They were. Later the system wouldn't boot up, and I saw the same 3 LEDs.
I was worried that I somehow broke the card while putting on the Accelero, but I decided to put the stock HSF back on and try it , just in case. Well, everything worked perfectly once the original HSF was back on!
After some research, the problem was that the VRMs were not being cooled enough. I had the heatsinks on them (from the accelero kit) but apparently those aren't good enough - you need really good contact, and active cooling.
So I'm currently stuck with the stock cooler. The noise isn't "that" bad - it's just louder than what I'm used to. To get the Accelero to work, I'm pretty sure I would have to cut (hacksaw) the original HSF, and keep the portion which covered the VRMs and other power circuitry. There are plenty of screws to keep this section of the HSF on all by itself, without the rest of the heatsink. Then I would install the Accelero and RAM sinks as normal.
A big pain, though. I would like to just buy a new original HSF for the card so I can hack that one up, keeping the original intact. For now, I'm downclocking the card on games which don't need much horsepower (which is just about all my games) and it's stays reasonably quiet, although the fan tends to foten get stuck in a state where it's constantly changing speeds. I will fix this by adjusting the fan profile...