You have to keep in mind that Kentsfield and Yorkfield are based on identical architectures. The die shrink provides lower temperatures, but no performance advantages in itself. The only 2 advantages of q9550 are larger cache and sse4.1, neither of which 3dmark cares for. All the reviews that shows Yorkfield being average 10% faster per clock are skewed by new video encoding programs that use sse4, which gives Yorkfield a large boost of 30%, sometimes even more.
Another thing is it's heavily dependent on your OS and amount of background load. My q6600 at 3.6ghz get a 4800, compared to your 5540. Vista Ultimate x64, with all kinds of crap running in the background, sucking up system resources. Take a look at the upper right corner of screenshot, nearly 1.5gb ram usage at idle.
http://ourworld.cs.com/dagger9066/screenshot002.jpg