first of all, thank you for your interest in our plugin.
I believe this works properly in our plugin. Wordpress always picks the category with the lowest ID for the permalink, if you use structure like /%category%/%postname%.html
So if you have parent and child category and you assign post to both, it will end up as /parent/postname.html if you assign only child category, it will be /parent/child/postname.html
If you are aware of this, then the issue must be somewhere else, perhaps some conflict with another plugin. Can you try to disable all the plugins and switch to default template and do the testing again?
There is a new version coming, which is in the final test stages: