The solution came from plugin author: I had to destroy and recreate the waypoints, so this:
$('#home .content').waypoint(function(direction) {
if (direction === 'down'){
$('#next').trigger('click');
}
}, { offset: 'bottom-in-view' });
Turn into this:
$('#home .content').waypoint('destroy');
$('#home .content').waypoint(function(direction) {
if (direction === 'down'){
$('#next').trigger('click');
}
}, { offset: 'bottom-in-view' });