function setCookie(key,value) {
    var exp = new Date();

    exp.setTime(exp.getTime()+(365*24*60*60*1000));

    document.cookie = key+"="+value+"; expires="+exp.toUTCString();
}

function saveSettings() {
// checkboxy
    for(var i=0;i<SETTINGS.length;i++) {
        setCookie("settings_"+SETTINGS[i],$("#settings_"+SETTINGS[i]).is(":checked"));
    }

// jeden input który nie działa
    var ses = $("#ses").val();

    if (ses) {
        setCookie("ses", ses)
    }

    $("#settingsModal").modal("hide");
}

if (isset($_SESSION['ses']))
{
    $ses = $_SESSION['ses'];
}

else
{
    $ses = '';
}

<div class="form-group">
    <label>test</label>

    <input type="text" class="form-control" id="ses" value="'. $ses .'" placeholder="test ...">
</div>