Actually, prompted by these emails, I think I know why the top menu is 
doubling. Well, this is a working theory, at least.

The CSS of Bootstrap is in conflict with the layout in Altitude. Similar 
to Seaside, you have one div for each component/class. The squeak.org 
prototype has two components, two columns: the menu bar on the left; 
and, the content section on the right. Both of them, I bet, are creating 
the top menu independently. It's being created twice and it appears when 
the screen scale shrinks.

The solution, would be to use rows instead of columns. Then make the top 
menu an Altitude component and the content section a component beneath 
it. I look into it in day or two.

Chris