The key phrase here turned out to be "segmenting my HTML into partials", as my problem is not related to Iron Router. Once you start placing HTML into templates, you cannot rely on the jQuery that is written into the theme to be aware of page updates that are the very essence of Meteor. For example, my theme contains the following code:
$('.menutoggle').click(function(){
// do things
});
This must in fact be changed to use the on()
function:
$(document).on('click', '.menutoggle', function() {
// do things
});
Or perhaps better yet, registered with my template:
Template.mypartialname.events({
'click .menutoggle': function() {
// do things
}
});