So having recently acquired a GTS 250, I'm somewhat disappointed to note that my PPD may actually have gone down on replacing my 9800GT 
I'm currently getting 4877 PPD on a 587 pointer with clocks at Core: 650, Shader: 1700, Memory: 875.
One of my 8800GTs is currently doing a 587 pointer (not a direct comparison, but pretty close) and is clocked at 700, 1800, 800 and is getting 5229 PPD.
Now by my reckoning, even assuming memory counts for nothing (which it doesn't), the 8800GT is set to <8% faster on the core and <6% on the shaders. Assuming it's 8% faster across the board, this gives an estimated 4842 PPD on the 8800 if clocked the same as the 250, which would be accurate if the 8800 and 250 were the same cards.
However, the GTS 250 has more shaders (128 vs 112) so as a rough estimate I should be expecting 5533 PPD from the 250 and 4842 PPD from the 8800, at equivalent clock speeds, which is over 10% more than what I'm actually getting.
Any thoughts on why I'm getting such relatively poor PPD? I noticed similarly poor PPD doing a 353 pointer as well

I'm currently getting 4877 PPD on a 587 pointer with clocks at Core: 650, Shader: 1700, Memory: 875.
One of my 8800GTs is currently doing a 587 pointer (not a direct comparison, but pretty close) and is clocked at 700, 1800, 800 and is getting 5229 PPD.
Now by my reckoning, even assuming memory counts for nothing (which it doesn't), the 8800GT is set to <8% faster on the core and <6% on the shaders. Assuming it's 8% faster across the board, this gives an estimated 4842 PPD on the 8800 if clocked the same as the 250, which would be accurate if the 8800 and 250 were the same cards.
However, the GTS 250 has more shaders (128 vs 112) so as a rough estimate I should be expecting 5533 PPD from the 250 and 4842 PPD from the 8800, at equivalent clock speeds, which is over 10% more than what I'm actually getting.
Any thoughts on why I'm getting such relatively poor PPD? I noticed similarly poor PPD doing a 353 pointer as well

. I also have SLI disabled and Physx enabled, but I've no idea if either of those settings make any difference. The only other thing to add is that I'm running under XP.