I've been using the track motion feature for a few weeks successfully. Now every time I try it will track a point through the entire clip but when it reaches the end the "Apply" button remains greyed out. Its possible my brain cells are playing up....
import mp4 video
create proxy to jpeg sequence (video)
run the track motion with 1 tracking point
tracking runs through all of the frames
screen shot attached - any suggestions appreaciated!
AE's tracker should default to the top layer, but its worth creating a null object and apply your tracked positions, scale and rotation to that. You can then parent the layers you want to this null object.