I've been looking at this a bit closer. The top group row of data is being given the class of rwmb-clone-template
which means it is being hidden. So looks like it has disappeared. This is rendered server side and has nothing to do with the JS files.
This group is submitted as the first in the group array since the fields in the group are legitimately form fields. But the server side code receiving it must be dropping this first group since it is expecting it to be a blank cloneable group and not a real value.
I've checked what is saved and confirmed that it is being dropped before persisting to the database.
I tried to follow the PHP to see where the $_POST object is being processed but seems to be quite a bit of coupling between the group module and the main meta box clone file that I couldn't find what I would looking for.