Sorry for double post, but my problem is solved thanks to @thomas’s help.
Apparently menu I created had parent_id “2” while my /var/www/html/app/code/MGS/Mmegamenu/Block/Mmegamenu.php
file was set to only show files with parent_id “1”.
So I went to phpmyadmin, found mgs_megamenu_parent database and simply changed the value from 2 to 1. And that fixed the issue, menu is now properly showed in the right place.
Again thank you very much Thomas 