Hi!
I just tested the original bones theme and both header and foooter work correctly.
Your code looks correct. At least you have the 'theme_location' parameter defined iw wp_nav_menu which is mandatory for Polylang to work. If your menus are correctly setup, it should work.
NB: There is a bug in v1.5 which prevents menus to be saved correctly from the customizer. So please use Appearance->menus to save the locations.