After a lot of research I finally found out that this was a bug with iOS safari and viewport units as described here: http://blog.rodneyrehm.de/archives/34-iOS7-Mobile-Safari-And-Viewport-Units.html
Rather than using viewport units to set the height of the pop out i've had to resort to javascript:
var viewportHeight = $(window).height() + 70;
var mobileNav = $('.header nav');
mobileNav.css({height: viewportHeight});
$(window).resize(function() {
viewportHeight = $(window).height() + 70;
mobileNav.css({height: viewportHeight});
});
After doing that, scrolling works as expected.