Tolerance
Use Tolerance to set how much tolerance for error there is in locating a match for the reference box. A keyframe is only set for the frame if a match is found.
If Tolerance is set to 100%, a match is always found, regardless of how wrong it may be. If Tolerance is set to 0%, a keyframe is only set for the frame if an exact match for the reference box is found.
A good rule of thumb is to leave Tolerance set to 100% and then lower it if necessary. It can save time to play your clip through several times and note where 100% Tolerance might cause the Tracker to lose the reference feature. You can then lower the setting for these portions of the clip.
For more information, see Adjusting Tolerance.