Please see the bug report at
https://github.com/jgoguen/calibre-k...iver/issues/19 and the related bug report at
https://github.com/jgoguen/calibre-kobo-driver/issues/7.
The TL;DR version is that this is a known issue that I can't do anything further about. There is a JavaScript file included in kepubs supplied by Kobo that I cannot distribute because the file is copyrighted and is not redistributable. This JavaScript file contains, among other things, functions to calculate the proper place to load the book from bookmarks and when you leave and return, and the proper place to put annotations. If Kobo wants to change the copyright on the necessary files, I'll include them in the plugin.