I think it boils down to similar issues like Trulli is having. Trulli's power steering is too assistive and he gets much less of an analog feedback and so his precision and instinctiveness can't help his qualifying. I don't think Mark has really been able to garner the desired feedback from the Pirellis yet. He mentioned in Singapore that the team made setup changes to help him; but I think that only helped him preserve tyres; and to be fair he's a LOT closer to Vettel now than he was at the start of the year in terms of tyre wear.
But I think he hasn't got the feedback he needs from the Pirellis. In high speed; when the car pretty much has a lot of grip everywhere, and not enough braking/torque to break traction and lock/wheelspin he doesn't mind, but I think if you look at a lot of the races this year in the slow stuff; where it's the tyres doing the job of gripping he's not really delivering - he's getting on the power too hard and causing wheelspin, he's getting on the brakes too hard and locking, and generally not carrying good apex speed. Which really puzzles me; as he is absolutely MIGHTY through the Norgard chicane in Nurburgring and the fiddly chicane at Barcelona.
Also another theory I've thrown around for a while now is that Mark; as by his own admission; prefers rear stability and less tail-happiness in a car. Seb on the other hand likes a strong front. I wonder if Mark is not too fond of getting oversteer from opening DRS too early, and is protecting himself from that by adding a bit of stability in the setup to the point of understeer. Bruno Senna was amazed at how much understeer Mark had in China qualifying this year too
It should be noted that these theories are purely conjecture and speculation