I also have the 08 disc and have a little shudder. When you spin your wheel and look at the rotor between the pads does the distance between rotor and pads stay uniform the whole way around? I suspect that if the rotor and pads aren't flush to one another that periodic fluctuation may cause some shudder. When I first got my bike the front rotor rubbed the outside pad slightly on each rotation. I adjusted the pad out a click to stop the rubbing, but I plan on realigning the front brake to really take care of it and I'm wondering if that'll fix the shudder as well.
The pads breaking in are also something to keep in mind. I've noticed a huge difference now that I've ridden a bit. The shudder seems less prevalent, but it's still happens.