Jeff- I'm no math expert, but since the gear ratio is 2:1, I would expect my mark to align from the beginning, then after revolution #1, the mark on the crank gear should be at its original location (meshed with the cam gear) and the mark on the cam gear would be 180 degrees away. Then the marks would align again after rotation #2.
So the marks will not "fade away" from each other in terms of # of teeth. Of course the marks will be moving at different rotational speeds (again, the 2:1), but the marks should always line up or be out of phase by 1 rotation.