When your script(main.js) is running the elements 'li.log-in, a.log-in'
does not exists in the dom, they are loaded dynamically when the popup is created thus jQuery is not able to bind the event handlers
Try event propagation
$(document).on('click', 'li.log-in, a.log-in', function() {
$.get('/login/', function(data) {
//make a modal window with the html
$.modal(data);
});
return false;
});