There are 2 possible causes:

1. The z-index value for the navigation menu (or site header) for your site theme is higher than normal.
   
   
   
   • Compensate for this by increasing the z-index value of your popup. 
   
   
   • In the Popup Editor, go to: 
     
     
     
     • ‘Popup Settings’ -> 
     
     
     • ‘Display’ option tab -> 
     
     
     • ‘Advanced’ option category -> 
     
     
     • ‘Popup Z-index’ selector. 
     
     
     
     
   
   
   • The default value for ‘Popup Z-Index’ is 1999999999. Add a few 0s to the end of each number. This increases the z-index value for the popup compared to the z-index value for the site theme. 
   
   
   
   

   This typically fixes a problem of this sort. 

   
   
2. Your site theme is likely including the WordPress function ‘wp_footer()’ inside a <div> with a z-index value not set to ‘auto’.
   • Locate the template file in your theme that contains the function ‘wp_footer()’. 
   • Locate the containing <div> in that template file, and find the z-index value assigned to that <div>.  
   • Change the z-index value of the page template <div> from an {integer-value} to ‘auto’.
   • Move the function ‘wp_footer()’ outside of the <div> container within the template file.