Tom,
Once you set your tracker boxes click the snap button, then analyze the track and stop it before the markers go off frame. If the track gets lost and the markers less the good reference, stop the track and use the backspace key to go back frame by frame and the bad keys will be deleted. Once you have stopped the track hold the control key and move the reference box to a new location with a good pixel reference, click the snap button again to set the reference pixels and then start the track again.
Ken LaRue
Autodesk Application Engineer
Training DVDs Composite and Combustion
http://www.thestreetproductions.com