When you get wrong answers the usual suspects are a driver bug or a bug in your app.

If you get the correct result when you use the reference device, it could be a driver bug. Many years ago (early D3D9 days) both NVIDIA and ATI had a bug where GetRenderTargetData didn't work correctly for small render targets (NVIDIA drivers could even freeze Windows in some cases). If it's a similar bug, you can do what I did then, which is report the bug and use a larger surface (such as 16x16) as a workaround.

If the reference device returns the same result, try checking PIX, to see where things go wrong. (You can probably just use PIX in the first place, if the reference device is too slow.)