It has to do with the encoding of the video.
Some codecs encode each frame independently, others mangle data from several frames to gain on the compression ratio.
For the latter case, the encoding is generally optimized for "forward decoding". Going back one frame means we actually have to go back to the previous key frame last full frame, then decode back all the way to the target frame.
MTS uses AVCHD which uses this technique and other more complicated patterns which sometimes confuses Kinovea to the point where the frames are not in order. Also, since this is HD video and decoding each frame takes some time, the issue is more visible than for lower resolution samples even if using similar encoding pattern.
If you are analyzing very short clips, you may constrain the working zone to 3 seconds or less, to trigger the "caching" of frames to memory.
Transcoding to an "intra-frame" only codec may also fix the issue. MJPEG is such a codec but there are others
edit: Oh, you mean it doesnt work at all ? Hum, yes, that might be one instance where the decoding process is confused. Ill have to dig deeper into this matter to see what is going onů
If you have the logs on Debug mode activated, you can see what it is trying to do and what is really happening.