If you can share the video privately it would be great to see where it falls short to improve the algorithm or the experience.
The core tracking algorithm in Tracker and Kinovea are fairly similar. They are both based on tracking a template inside a search area and update the template based on some heuristics.
Depending on the failure case you might try different values for the match and update thresholds. This is how Kinovea controls template update (Tracker uses different mechanics with "evolve" and "tether").
For example if it gets the wrong marker too often you can increase the "match threshold". When it fails and you replace it manually it will reset the template.
I see now that it doesn't actually stop the playback when it looses tracking, I agree it probably should, I think this behavior was changed at some point. I'll fix that or at least make it an option you can toggle on/off.
You can also increase the update threshold to 0.85 or 0.90, if the tracked object visually changes a lot this will update the template more often and can improve things.
One of the most important thing is that the object window, which defines the template, should be as tight as possible around the physical marker to avoid picking too much background (but still have some details in it). The search window should be large enough to cover marker motion but not too large that it might get confused with another marker.
A round shaped marker will work better (in both software) because an "X" shape will vary under rotation. (we don't look for the rotated template, only slide the template inside the search area and compute a score based on pixel correspondences).
If you can share the video with me I would love to test it.