Well, I've just changed the Gipiemme wheels on the Cannondale CX to the OEM Bianchis that came on a new road bike, basically just to see if the different wheelset would change anything.
It did, in that the shudder is now much more pronounced, the good thing is it's now very easy to see from the saddle that it's definitely the carbon fork flexing about half an inch or so back and forth when the brakepads are applied with anything more than the very gentlest touch.
I'd agree with jpearlk above that this fork/brake combo is obviously only intended for the lightest tapping on loose surfaces - that's all it can do, due to the fork flex/chatter it has no effective stopping power compared to a normal MTB or roadbike.
I can and have been riding the bike around town as well as on trails etc, but I do have to constantly remind myself to leave more emergency braking space in front of me compared to my road bike.
Whether this is acceptable performance for an ex-factory component combination I don't know.
I also still wonder if there's more going on, i.e. whether my carbon fork has a defect of some kind that makes it flex so much under what's in reality moderate braking. The amount of flex happening is pretty impressive for such a big/solid looking carbon fork. If it's not prohibitively expensive, I may try buying a replacement from Cannondale to see if there is a difference. The rest of the bike's so enjoyable that it's worth some effort.