That is the exact result I am seeing as well.
I don't know why some are getting lower PPD on bigger units.
I'm seeing it on all four Q6600s. One is 3.2, another is 3.4 and the other two are 3.6. Every one of them has gotten the 6040s and 6041s and they all see a drop in PPD. I do see somewhat better PPD with the 6041s than I do with the 6040s but the 6041s still have a drop compared to the regular A3s.
This has nothing to do with the GPU client either. I've shut off the 8600GT on one system and the PPD didn't change at all. I shut off the 8800GT on my main system and saw maybe a 100PPD increase when I did that. I actually see larger PPD jumps when killing the GPU client while processing the regular A3s.