Having trouble setting / modifying cookies

if (getCookie($(this).attr("id")) == true) {

The above code will NEVER evaluate as true because cookie values are stored as strings. You are trying to store a boolean value, which is converted to a string when it is written to the cookie. When the browser reads the cookie value, it is also read as a string.

The fixed version of your code should be:

$('.ss-show-collapse').click(function(){
    var collapse_anchor="."+$(this).attr("id")+' span';
    show_collapse=".ss-show"+$(this).attr("id").replace('ss-show-collapse', '');
    $(show_collapse ).toggleFade('slow');
    $(collapse_anchor).toggle();
    if (getCookie($(this).attr("id")) == 'true') {
        setCookie($(this).attr("id"), 'false', 1);
    } else {
        setCookie($(this).attr("id"), 'true', 1);
    }
    return false;
});

I would also suggest looking into using event.preventDefault(); instead of return false; http://fuelyourcoding.com/jquery-events-stop-misusing-return-false/

$('.ss-show-collapse').click(function(event){
    var collapse_anchor="."+$(this).attr("id")+' span';
    show_collapse=".ss-show"+$(this).attr("id").replace('ss-show-collapse', '');
    $(show_collapse ).toggleFade('slow');
    $(collapse_anchor).toggle();
    if (getCookie($(this).attr("id")) == 'true') {
        setCookie($(this).attr("id"), 'false', 1);
    } else {
        setCookie($(this).attr("id"), 'true', 1);
    }
    event.preventDefault();
});