Well firstly we have no access to this template so i cant see template options nor template codes..
Only thing i can suggest is look for top menu code in templates php files as its loading menu name rather then menu position or module position so you have two positions which loads same menu name , so change the second one to whatever the second menu name is...
I still suggest you get more help / support from templates creator as this is a template specific question regardless of the mods freelancer have done on it...