If it is indeed a similar issue than bug 214, then yes, the problem is during saving the file to MKV.
We specify the initial fps, for example 29.97fps, and it is somehow changed to 30fps (only some specific fps are subject to the issue).
The final video contains the same number of images, but they are not aligned with time anymore.
Seeing the large shift and the fact that it goes the other way, your issue may be a different one.
Also, if you didn't reencode the .asf and when reopening the key images are still offset, then it is definitely a different issue.
If possible, create a very short video on the camcorder, like 1 or 2 seconds, and do your conversion to .asf.
Then attach the .vob and the .asf to bug 214, or send them by mail to: joan at kinovea dot org. Thanks 
Also, the .vob might be readable directly in Kinovea if it's an option.