@MockoB I think I located the bug.
When there are no categories at all, if you click on the expend all button if will get broken ajax result, which cause the bug the you are experiencing, due to the fact that the return ajax result will change the category tree input name from id_parent to something else and because of that the controller will create a root category instead of regular category with Home as parent.
Basically if you work as usual and won't click the expend button (before adding a single category) you should be fine.