Crysis 3D will be most likely Side-by-Side 3D, which means it basically splits the screen and halves the horizontal (x) axis. With the two pictures overlaid on the different layers of your screen, you do see a full screen, but it's actually a picture half as wide. As such, when moving the camera left or right, the space between the sides is only half, but the sensitivity (at least in Crysis 2) stayed the same. Which meant that the speed of moving the camera left and right is twice as fast as up and down.
If the game does not compensate for that, there needs to be an option to manually adjust your x-axis and y-axis sensitivity.