Given that this has occurred on two brand new bikes, I think its probably safe to rule out a wobbly wheel or loose headset as the cause. My guess is that the shuddering is caused either by poor brake setup, low quality stock brake pads, or braking technique. Getting good braking with cantilevers and road levers is not easy. And even when set up well, the modulation will never be as good on cantilevers as sidepulls. This means you have to pay attention to how you are squeezing the lever. You're probably pulling the lever too hard.
A good experiment would be to ride on flat ground at 25-30 kph, pull the levers enough so that the pads just start to touch the rims. Once they are in contact, very gradually increase the pressure, and note the point at which the shuddering occurs. My guess is you will find an amount of lever pressure that provides adequate braking, but doesn't cause the shudder. If that doesn't solve the problem, your brake setup probably has too much leverage. Here's a good guide to adjusting cantilevers:
http://www.sheldonbrown.com/cantilever-adjustment.html
It took me a while to get good at tweaking cantilever brakes, but now I'm a whiz at it. It just takes some experimentation.
I should also add that the stock pads on most brands of brakes are not good. I've had very good luck with Kool Stop MTB pads.