When a track goes awry, you do not manipulate the Surface, you should instead manipulate the tracking spline shapes.
The Surface is where you define the area that you will be exporting. When you export, you have a choice of either Transform or Corner Pin data.
The Surface area does not affect what Mocha tracks. It is the shapes defined by your X or B-splines that tells Mocha what to track. Hence, when you re-define your Surface on a single frame, the duration of the track is affected by this change. Mocha thinks that the new Surface is what you want to export, hence the entire duration of the track is affected.
What you should do instead is to adjust the tracking shapes.
Further, your track goes awry when the rotation kicks in. This is where you manipulate the Rotation parameter. Adding Rotation adds to the tracking time. Therefore, you can start with a value of 0 and then dial in a value just as the rotation starts. You then re-set Rotation down to 0 once the rotation is completed.
You can watch a related tutorial here -
http://www.imagineersystems.com/videos/mocha-pro-tracking-large-rotation/vi...
HTH
RoRK
Intensive AE & Mocha Training in Singapore and Malaysia.