Hi,
we are using the WP importer 2.0 (https://github.com/humanmade/WordPress-Importer) as the core WP importer. At the time of development of our plugin it was worked on quite extensively and it looked like it will replace the old importer…
The WP importer 2.0 project has now been on “pause” for a good amount of time and we don’t know, if it will be worked on at all… It has a lot of performance improvements, but it also has a few bugs.
Maybe this is one of them. However, we never had issues with menu imports. The hierarchy of the menus was always imported as it was in the original, so I don’t know, why this would not work for you as well.
Are you using any WP menu plugins, which might cause these issues?
Take care!