The Tolerance value determines how much discrimination the Stabilizer uses in matching the reference point from frame to frame and in setting a keyframe for that frame. At 100% tolerance (no discrimination), almost anything is considered as a match and a keyframe is set. At 0% tolerance (complete discrimination), only a perfect match is accepted.
If the reference point becomes hidden by another object, you can use the Tolerance value to make the tracker ignore the reference point in parts of the clip where it is hidden, then continue tracking it normally when it reappears. Choosing a good Tolerance value reduces the need to manually reposition the tracker box during analysis.
To find the best Tolerance value:
The crosshair reappears when there is a keyframe.
Once you determine the optimal tolerance value, further analysis automatically discards the undesirable keyframes, and the position of the reference point is extrapolated until the reference point reappears.